How to Amend Garden Bed Soil: Organic Fertilizer, Compost and More

By Deanna Talerico Mar. 20th, 2025

Out with the old, in with the new! Come learn how to refresh and amend garden soil, with tips to prepare a new or established raised garden bed for planting.

This article explores the the best way to remove old plants from the garden, when and how often to add fertilizer, our favorite organic fertilizer and compost options (and other natural amendments), and the step-by-step process we use to amend our garden beds before planting.

Soil health is KEY to the success of a garden, and should never be ignored! With these tips, your plants will grow bigger, stronger, and more productive than ever.

Starting with a brand new bed? Come learn how to fill a raised garden bed with organic soil and compost.

Note: This post was originally published in October 2019 but significantly refreshed in 2025.

Two hands are held together cupping a large handful of compost that is in the shape of a heart. A bed of lettuce growing is beyond.

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Removing Old Plants from the Garden

When it is time to remove old plants from a garden bed, we prefer to follow a “no-till” or no-dig method most of the time. Rather than pulling plants out by their roots, we cut them out at the soil line or just below and leave the roots to decompose in place.

To cut out old plants, we use sharp pruners or a small hand saw, depending on the size and toughness of the stem. The roots will break down over time, providing food and nutrients to the plants, along with the worms and other beneficial microorganisms in the soil!

No-till farming offers numerous benefits to soil, such as improved biological diversity, fertility, resiliency, water retention, organic matter, and nutrient cycling. In contrast, tilling soil increases erosion and disrupts the natural soil structure and beneficial life within.

If the spent plants aren’t diseased, we add them to our compost bin (or share some with our backyard chickens, when edible and appropriate). Otherwise, they go in the green waste.

RELATED: Learn more about no-till gardening here, including when it may be a GOOD idea to lightly till your soil too (such as to combat root-knot nematodes).

A man is leaning over a garden bed with a hand saw, he is sawing the stems of plants off at the soil line, leaving the roots behind in the soil. The plants resemble trunks sticking out of the soil, these were leafy green vegetables or cauliflower and there greens have all been striped from the plant. There is a half wine barrel with carrot greens sprouting out of the top in the background, along with various other pollinator plants, trees, and shrubs. — Aaron removing old broccoli and cauliflower stems, using a small saw to cut the dense stalks at the soil line.

Why Amend Soil?

As plants grow, they draw up essential nutrients from the soil, leaving it low or even depleted by the end of the growing season. So, it’s important to replenish nutrients so the next round of plants can thrive! To do so, gardeners typically apply fertilizer and/or compost each year (or more often).

Some amendments are also used to improve soil texture or drainage, not just nutrients. For example, you can add compost and/or potting soil to fluff up dense clay soil or to improve moisture retention in sandy soil.

Crop rotation and cover crops can also be used to enhance organic soil health and nutrition.

A graphic with a tomato growing showing organic fertilizers on one side and synthetic fertilizers on the other. The synthetic only offer plant nutrients while the organic offer organic matter, soil nutrients, plant nutrients, and micro-organisms. — As organic gardeners, we always focus on feeding the soil – not just the plant! Promoting long-term soil health is more sustainable, long-lasting, lower maintenance, and most beneficial for your garden. Synthetic fertilizers offer a quick “fix” but higher risk.

When To Amend Garden Soil

Most gardeners amend their soil in spring, just before planting time. Ideally, plan to add fertilizer a week or two prior to planting, giving it time to mellow out before the plants go in. (This is especially true with strong fertilizers like bone or blood meal that pose a risk of burning plants. Since we use more gentle options, we sometimes fertilize immediately before planting without issue.)

However, amending too early can be wasteful. For example, if you apply fertilizer in the fall and leave the beds empty all winter, rain will wash away much of the added nutrients.

We live in a temperate climate and garden year-round, so we amend our beds twice per year – once in early spring and again late summer before planting fall crops.

It can also be helpful to offer heavy-feeder crops additional fertilizer once or twice during their growing season. We’ll discuss ways to feed soil mid-season in the “fertilizer options” section to follow.

Deanna is squatting next to a raised bed as she plants lettuce seedlings in a row. Aaron is standing next to her as he removes the seedlings from their containers. — Since we garden-year round, we amend our beds twice per year. Here we are planting fall crops (lettuce) in a freshly-amended raised bed at the end of summer.

How to Amend Garden Soil Before Planting

If you haven’t already, clear out old plants from the bed. Also remove any weeds or other debris as needed. Again, we avoid tilling or digging unless necessary. If your garden beds are mulched, you may want to pull back the mulch before applying amendments and then put it back on top afterwards.
Again, we generally avoid turning or tilling soil. Yet if the soil level has sunk significantly in the bed (common in newer raised garden beds), we sometimes add more fresh soil before the next compost layer.
Next, add a slow-release organic fertilizer of choice. (See discussion about various fertilizer and compost options below.) Sprinkle it evenly across the soil surface, and then scratch or lightly work it into the top couple inches of soil with your fingers. I recommend wearing gloves, and use just slightly less than the suggested amount on the package.
Now, we top off our raised garden beds with 1 to 2 inches of well-aged compost, which also doubles as our mulch of choice.
Finally, water the soil thoroughly to help the fertilizer seep in. It will continue to break down and release nutrients over time.
Ideally, wait several days to a couple weeks before planting.
We also incorporate a few additional soil amendments at planting time, such as adding worm castings and mycorrhizae sprinkled right in each planting hole. Both help to reduce transplant shock, increase nutrient uptake, and encourage fast healthy root development!
After planting seedlings, be sure to mulch the top of your soil! Mulch helps soil retain even moisture levels, suppress weeds, and protect plant roots from temperature extremes. About 2 to 4 inches of mulch is (ideal depending on the type).

RELATED: Don’t miss our top tips for transplanting seedlings, or learn more about the pros and cons of 8 popular types of garden mulch here.

The raised garden bed have no plants growing in them after they have been removed. The raised bed in the foreground has fertilizer sprinkled over the top of it to amend the soil. — A sprinkle of well-balanced organic fertilizer on top of the soil

A hand is being used to scratch in fertilizer on the top of garden soil to amend the raised bed. — Lightly work/scratch it into the top couple inches

A half teaspoon of mycorrhizae is held above a transplant hole with a trowel and seedling laying next to the hole. — We add a small handful of worm castings and sprinkle of mycorrhizae to each planting hole. Mycorrhizae is a beneficial fungi that colonizes on plant roots, helping them take up nutrients and water more efficiently while also protecting plants from stress, drought and disease. It needs to come in direct contact with roots right away, so it’s most effective applied right around the rootball.

A raised bed garden space with many young seedlings growing in each of the raised bed. The beds have been topped with a fresh layer of compost and mulch. — A couple weeks later, after adding compost/mulch and planting new seedlings

Fertilizer Options

There a number of ways to fertilize garden soil, and every gardener has their preferences! We like to use natural amendments, compost, and gentle, slow-release, well-balanced organic fertilizer (e.g. 4-4-4) instead of stronger options like blood meal.

It’s better to go light than accidentally overdo it and “burn” or shock young sensitive plants! You can always add more, but it’s difficult to take excess away. Plus, fertilizer isn’t the only way we maintain soil health.

With our gentle fertilizing methods, we treat the soil in all of our raised beds the same from the start. Then, we provide heavy-feeding plants (e.g. tomatoes, corn, squash, melon, garlic) additional nutrients throughout the growing season as needed with homemade compost tea, dilute seaweed extract, alfalfa meal tea, or a side dressing of more slow-release dry fertilizer.

TIP: When looking at fertilizers, you’ll notice three numbers (such as 6-3-1). This is the NPK ratio, which shows the respective level of nitrogen, phosphorus, and potassium in the fertilizer.

A glass measuring cup of alfalfa tea held in front of a raised bed full of Swiss chard will be used to amend soil. A 5 gallon bucket of alfalfa tea sits next to the raised bed. — A fresh batch of homemade alfalfa tea, to feed select heavy-feeding plants mid-season

Compost Options

Compost is dark, crumbly, nutrient-rich material derived from decomposed organic matter such as food scraps, yard or garden waste, leaves, straw, cardboard, or certain animal manures. When added to soil, compost improves soil structure, fertility, moisture retention, and promotes healthy plant growth. We’ve used a wide variety of compost options over the years: bagged, bulk, homemade, worming castings, and more.

Worm castings (aka “black gold”) is a top favorite, which you can make at home with an easy DIY worm bin or purchase in bags. A little goes a long way! If you add worm castings to amend garden beds, you’ll only need a light sprinkle over the soil (not inches deep like other compost). Or, simply add a little handful to each planting hole like we do. It’s best to use worm castings in addition to other forms of compost, not as the sole amendment.

In addition to our worm bin, our current main source of homemade compost is well-rotted manure from our mini donkeys, mixed with some garden waste and chicken manure. It all sits to decompose in our DIY compost bin for over a year. If you do choose an animal manure-based compost, make sure that it is thoroughly aged! Many types of fresh animal manure can burn your plants.

If you can’t make your own, you should be able to find some good compost locally – either in bags or bulk. Often available through local landscape supply companies, bulk is most affordable for large projects. For bagged, I generally prefer the quality compost options at local nurseries or “grow shops” over big box stores.

Our favorite bagged compost is California-based Malibu’s Compost, made from certified organic dairy cow manure and biodynamic plants. (Yet it’s fairly spendy so we’ll usually add just a bag or two per bed in addition to another compost option.) Coast of Maine is a similar premium option for the east coast.

RELATED: Learn composting basics along with six different ways to compost at home here, including compost tumblers, worm bins, hot or passive piles, and more!

Four mini donkeys are standing around a 3 bay compost system full of manure. A wheelbarrow is in the foreground which contains aged donkey manure to amend raised beds. — Our donkey girls “helping” us harvest their composted manure

Before we had a larger property and donkeys, we still had a worm bin, compost tumbler and smaller single-bay compost pile, but still didn’t make enough homemade compost to meet our needs. Malibu’s to the rescue!

And that is how we turn over our garden beds and amend soil between seasons.

I hope you found this article useful and learned something new! Always feel free to reach out in the comments with questions, feedback, or just to say hi. Thanks for tuning in, and happy planting!

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101 Comments

Alisha

February 26, 2023 at 7:43 pm Reply

I live in zone 3b. I have raised garden beds. The past few years my garden looks beautiful but doesn’t produce anything! Any suggestions?
- Aaron (Mr. DeannaCat)
  
  February 27, 2023 at 10:49 am Reply
  
  Hi Alisha, that’s too bad to hear but there could be a number of reasons that this occurs. Since you are in zone 3b, you likely have a very short growing season, it is best to focus your attention on plants that can produce fruit in a short maturation period. An example for tomatoes would be to stay away from any varieties that take 80-90 days to mature and look for varieties that only take closer to 50 days before they ripen. Not sure if you start your own seeds indoors or direct sow them outdoors or even get seedlings from the nursery, but starting seeds 6 weeks or so before your last frost (depending on vegetable type) will ensure that your plants are bigger and ready to plant out into your garden when the timing is right as opposed to waiting to direct sow into your garden when the weather turns. Another issue could be too much nitrogen in your soil which will lead to heavy leafy plant growth at the detriment of your plants setting and producing fruit. Again, there can be couple reasons for the issue that you have had the last few years so any more insight you can provide on your situation will help us narrow down what issues you may be facing. Hope that helps and reach out if you have any other questions.
Dan

September 8, 2022 at 9:28 am Reply

DeannaCat/ Aaron,

I live in Zone 10a and would like some advice regarding Cover Crops.

Should I plant more than one and/or a mix of Annual and Perenial?

Thanks,
Dan
- Aaron (Mr. DeannaCat)
  
  September 8, 2022 at 12:15 pm Reply
  
  Hi Dan, it just really depends on what you are planting the cover crop for. Do you intend to plant out veggies or other crops in the soil or leave it for cover crop alone? We like to use fava beans, an oat and pea mix (some have vetch included in the mix as well), buckwheat, winter rye, or barley. Most of these should be decently winter hardy for your mild growing climate. For your case, I would look for a mix that offer multiple benefits. Just be sure to cut down the cover crop before it goes to seed if you don’t want it to reseed itself. Hope that helps and good luck!
Russell Bischoff

August 21, 2022 at 1:12 pm Reply

Hi I have a question about outdoor cannabis I live in Mi and after the season is over and after ammending the soil can I plant new seed in the fall and let them pop in the spring on their own. I am in zone 6A.
I love your site its a goto for me.
Thanks Russ
- Aaron (Mr. DeannaCat)
  
  August 23, 2022 at 3:28 pm Reply
  
  Hi Russel, I wouldn’t advise you germinate your seeds this way as the winter months will be quite brutal and even if your seeds do sprout come spring, if you are hit with a late spring or early summer frost, your seedlings will likely die because of it if left unprotected. If you have a lot of seeds that you don’t care as much about, you could always sow some seeds come fall and see how the experiment goes. Hope that helps and have fun growing!
IreneKF

August 21, 2022 at 12:08 pm Reply

Thank you for all the information about preparing beds for planting. I am learning so much from you!
I have 3 long raised beds that I left fallow for about 5 years. I live in Zone 9 and the native soil here is clay. Last year, I dug in some dry leaves but that didn’t make much of a difference. This year, I planted a few tomatoes and some marigolds, but they are not thriving. I have been making compost for a couple of years using large garbage bins with holes drilled underneath and all around the sides, alternating green waste with shredded leaves and twigs from an arborist. It is looking very good.
I have purchased Borage seeds to plant as a cover crop and will probably buy some different seeds as well. At this time I don’t have room to plant Comfrey, but maybe next year.
My questions:
1. Should I spread the compost before or after growing the cover crop?
2. How would you recommend applying the compost? Dig it in or spread it on top?
3. What kind of worms would be best to purchase and how do I incorporate them into my soil?
Thanks again for your wonderful articles.
Irene
- Aaron (Mr. DeannaCat)
  
  August 21, 2022 at 1:14 pm Reply
  
  Hi Irene, it’s great to hear you are making your own compost! Borage is a great dynamic accumulator but they can easily reseed themselves if they go to flower, it really isn’t that big of a deal but just something to consider, I like using oat and peas for a cover crop as well where it is chopped down just before it goes to seed and is used as a green manure. As far as your questions go:
  
  1 & 2. Since your beds don’t seem to be thriving just yet, I would try and work in a decent amount into the soil itself while also spreading an inch or two over the top of the soil as well.
  3. We vermicompost and when adding castings or even worm tea to our garden, a few worms invariably end up in our garden soil, these worms are called red wrigglers. We have also just added a small handful to a garden bed and covered them with soil. They will regulate their population depending on the environment they are in. However, if you live in a heavily forested area with a lot of forest duff, if they get out of the beds and into the wild, they can have a negative effect on the environment as they will eat the decaying material on the forest floor at a faster rate than the native worms and other insects. If you have earthworms in your area, those can be added as well but they aren’t as voracious of eaters as red wrigglers, nor do they produce as much castings.
  
  Hope that helps, ask any other questions you may have and have fun gardening!
Jan`

August 21, 2022 at 7:14 am Reply

Thanks for the wonderful information. We live in Zone 7A, have multiple raised beds and a greenhouse in Zone 7. My question is about your drip system for your raised beds. Is the drip hose in each bed separate or can you water several beds at once? Would you describe your watering system more fully? It sounds so much easier than what we do. Thanks!
- Aaron (Mr. DeannaCat)
  
  August 21, 2022 at 7:54 am Reply
  
  Hi Jan, in our old garden we used the soaker hoses in a few beds and we had to connect a hose directly to each of them to water. If we tried to use a 2 way hose connector to run two at once, it didn’t have enough pressure to water the beds adequately. We have a new property and garden now and now use drip tape irrigation to water our raised beds, if you want to look more into it check out this article: How to Install Drip Irrigation in Raised Garden Beds (Drip Tape) or we have an article on how to hook up drip to a hose spigot as well: How to Connect Drip Irrigation to a Hose Bibb (Spigot or Faucet). Hope that helps and good luck!
Kathy

July 10, 2022 at 11:19 am Reply

I thought I had amended my soil enough this year, but for whatever reason, I have a lot of stunted plants that just failed to thrive. Even my zinnias are bad this year. I’m sure there are multiple reasons, but I’m wondering if it’s my soil. I’ve read in other places that soil tests are always a great idea. Have you done this, and if so, how? I’m not even sure where to start, or find resources/vendors close by that would test my soil for me. I cant help but be dissapointed in my sad garden this year! Thanks in advance.
- Aaron (Mr. DeannaCat)
  
  July 11, 2022 at 8:29 am Reply
  
  Hi Kathy, that’s too bad to hear that you are having trouble with your garden this year as that can be very disappointing. We think having a worm bin and using the vermicompost in compost tea can really help build the microbial life in the garden. We have done the at home soil tests but they aren’t usually too in depth and I am not sure how accurate they are either. You can always send in soil samples to have them lab tested, here are a couple links to companies that we are familiar with: Arbico Organics and Logan Labs . Hopefully that helps to get you started and helps you get your garden back on track. Reach out if you have any other questions and good luck!
Lucinda

March 20, 2022 at 9:46 am Reply

Hi Deanna and Aaron – thank you for this and all of your great content. I reference your website all the time and have learned so much from you. Last year I had the space to start my first real veggie garden and I’m getting ready to plant anew for spring (I live in zone 5b in Maine so no winter plants for me). I followed the advice in this article to overwinter my beds and added a layer of compost and then a thick layer of woodchip mulch on top of that. I’m happy to report that the soil underneath that has now thawed is looking GORGEOUS and healthy and I know it would have eroded so much if I hadn’t tucked it in with all that mulch.

But now that I’m getting ready to plant I’m trying to figure out if I should remove the woodchip layer or just leave it and work on top of it? It seems like if I added fresh fertilizer and compost on top of the wood chips it might not work into the soil, and that it could make tasks like direct sowing seeds like radishes tricky. Do you have advice? Thank you!
- Aaron (Mr. DeannaCat)
  
  March 20, 2022 at 12:32 pm Reply
  
  Hi Lucinda, that’s great to hear you had such success with overwintering your garden! The wood chips will eventually break down into organic matter for your garden but in the meantime it may be in the way. If you can, rake away what wood chips you can from your garden area before applying amendments and compost. You can always use the wood chips to re-mulch your garden space for areas that aren’t going to have directly sown veggie seeds. If you are going to plant radish seeds, it is easiest if you don’t have to compete with the wood chips for seed placement. Hope that helps and good luck on getting your garden going this season!
  - Lucinda
    
    March 20, 2022 at 5:07 pm Reply
    
    Thank you! That was my impulse but I couldn’t find a clear answer anywhere. Thanks for the quick reply and happy spring equinox! I’ll be planting those radishes soon 🙂
Heather Cortez

March 7, 2022 at 9:03 am Reply

Hi,

Thanks for all the great information!
I am getting ready to amend my raised beds. Can you suggest a good dry meal fertilizer?

Thanks!

Heather
- Aaron (Mr. DeannaCat)
  
  March 8, 2022 at 7:35 am Reply
  
  Hi Heather, if you want an all in one amendment mix I would look into Down to Earth’s All Purpose Mix, their Vegetable Garden Mix, or the Vegan Mix, or another brands similar product. Good luck!
Deanna

February 20, 2022 at 9:28 am Reply

Hi – I am in a situation where I am constantly rotating crops out of my beds all year long (we have a lodging property that offers our veggie gardens for guests to harvest to compliment their meals). This means I have to be diligent about crop rotation, regenerating the soil, and cover crops when I can fit them into the rotation. I typically use a very healthy amount of compost when I turn my beds, but haven’t been fertilizing until my toddler seedlings have been in the bed a couple of weeks. At that point I use a liquid fish fertilizer. With all of this said, I am constantly trying to improve my soil and my overall plant health. I see that you use a mix of many fertlizers when turning your beds and I am curious as to why so many as opposed to a mix? Also, if I understand correctly you are only doing this twice a year – spring planting & fall planting. So, I would probably not do this much fertilizing every time I rotate a bed since it’s much more frequent. Do you recommend I use an additional fertilizer at planting time? I’ve tried the micchorizae you’ve recommended in the past but didn’t notice a difference (perhaps I did not use it consistently enough..). I do appreciate all your knowledge and love following your journey. Thank you in advance for my long ramble of questions.
- Aaron (Mr. DeannaCat)
  
  February 20, 2022 at 10:58 am Reply
  
  Hello Deanna, we typically amend the beds twice a year but will occasionally top dress tomatoes, peppers, and squash with a smaller amount of amendments every month or so during their growth. A pre mixed amendment is easier to use for most people but we like having the ability to make botanical teas or top dressings of specific amendments if we so choose, it is just easier for us to have multiple types of amendments to have on hand to use as we see fit. We make and use compost tea throughout the growing season, usually every month or two and that helps improve your soil which will in turn benefit our plants. Hope that helps and good luck!
Russ Verkest

December 28, 2021 at 4:41 pm Reply

It’s the end of December, 2021 in Georgetown, TX. I have green beans in one raised bed, and peas in another. Will be needing to clear the beds and amend for my early 2022 crops of lettuces, arugula and onions in the green bean bed, and Potatoes, and later Corn in the Pea bed. How many weeks before I actually plant the new seeds (or seedlings) should I cut down the currently growing beans and peas?
Although I did fall plantings with Nitrogen fixing crops, I will still amend with organic cow manure compost and worm castings. I will also use granular organic all purpose Espoma fertilizer, but will go light with it.
Should I leave the bean and pea roots in place and just cut off the tops just below the surface?
Any other suggestions?
I really enjoy your website, emails and excellent information you provide!
Blessings!
- Aaron (Mr. DeannaCat)
  
  December 29, 2021 at 8:09 am Reply
  
  Hi Russ, we are glad you find the website informational and we appreciate your support! We would cut down the crops at the soil line (leaving the roots in place) anywhere from a week before to the day of amending and planting, whatever is easiest or works best for you. It sounds like you have a good system going and your additions should keep your garden flourishing. Your peas are the one crop that doesn’t need a lot of fertilizer but your other crops may like a mid-season top dress. Hope that helps and have fun gardening!
  - Russ Verkest
    
    December 30, 2021 at 6:22 am Reply
    
    Thanks! May you and Deanna have an amazing, safe and healthy 2022!
  - Laura
    
    January 17, 2023 at 7:11 am Reply
    
    Hi Deanna, what a great informational post! I too prefer no-till gardening as much as possible. Thank you for your information on how to amend soil. I often forget about this step but it’s so important! Love your hoops and netting system too…what a great idea! Thanks again for writing this post!!
    - Aaron (Mr. DeannaCat)
      
      January 17, 2023 at 8:20 am Reply
      
      That’s great to hear Laura and yes, amending your beds with compost and or slow release organic amendments can help out a lot in the garden. Thanks for reading and have fun growing!