How to Amend Garden Bed Soil: Organic Fertilizer, Compost and More
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.
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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).
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.
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.
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.
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.
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!
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!
You may also enjoy:
- How to Plant Tomatoes: When, How Deep, Fertilizer, Pots & More
- Garden Companion Planting Chart, Plans, and Benefits
- Vermicomposting 101: How to Make a Simple Worm Compost Bin
- How to Practice Crop Rotation (Garden Benefits Explained)
- How to Build a DIY Compost Bin: Step-by-Step Guide with Photos
101 Comments
ILA SHARMA
Hi , loved going through your blog. Can you please tell some amendments for a potted garden ?
Thanks.
Aaron (Mr. DeannaCat)
Hi Ila, the amendments we typically add to our garden beds are kelp meal, neem seed meal, alfalfa meal, crab or crustacean meal, and basalt rock dust for remineralization. To make things easier, you can find an all in one amendment that is a mixture of multiple meals. Look for ones that are mild and slow release and opt to use less than what is suggested on the label of the product. Hope that helps and good luck!
Jack
Hi Deanna and Aaron, Thankyou very much for posting all of this info! I just created a new raised bed, and filled it with a mix of “raised bed mix” and 2 types of compost, one being mushroom. Mostly will plant next spring, but was going to do some fall lettuce (zone 5b). Will the mushroom compost kill my lettuce seeds ? Thanks jack
Aaron (Mr. DeannaCat)
Hello Jack, since mushroom compost can have a high salt content and can potentially harm germinating seeds it may be best starting the lettuce seeds in smaller pots and then transplant them into your raised beds once they are healthy seedlings. Good luck and thanks for being here!
Jack
Thankyou !
Barry Sherwood
like your food growing, preparation, storage, canning, drying, planting – essentially everything – i think one of your blogs/videos was about saving seeds – i have some pole bean pods which dried on the vine and have harvested the seeds – have other pods not dried but with obvious seeds – will those pods dry and the seeds be viable for planting
Aaron (Mr. DeannaCat)
Hi Barry, it is best to let the pods dry on the plant when trying to seed save, you can always keep the other pods around and let them dry off the plant and see if they germinate next year. Good luck!
Kim Strassmann Eagle
This blog post could not have come at a better time! It is exactly what I needed to know as I get ready to amend my elevated raised beds for my Fall garden. Would you recommend putting down the fertilizer and a layer of compost a couple weeks before I plant my seedlings? or just the fertilizer and put fresh compost down the day I plant the seedlings?
Aaron (Mr. DeannaCat)
Hello Kim, amending your soil and topping it with compost a couple weeks before you plant out your seedlings is a great idea! It will allow the amendments to break down into the soil slightly before the new seedlings are introduced. Just be sure to err on the lighter side as to not burn your plants or stunt them unnecessarily with too much amendments. Good luck and have fun!
Lillian
How do you keep rabbits and rats from eating your produce.? We live in Southern CA and have tried everything to repel them. We have stiff wire around the raised beds but they just climb up. We put netting on top but somehow they get in. They will eat newly planted peppers right down and I have very few tomatoes. The only ones I get are the ones in the tipsy turvy planters .
We tried traps but we have a dog so have to be careful.
Aaron (Mr. DeannaCat)
Hello Lillian, unfortunately we don’t have to deal with rabbits at all and rats are only a small issue, we usually find some rat presence in our passion fruit vines but they normally stay away from our garden areas. Maybe raised garden beds or fencing would keep rabbits from accessing your vegetables? As far as the rats go, keeping your garden tidy as well as any areas that may harbor the rodents is a first step. Peppermint oil is said to deter rats so maybe using cotton balls that have been doused with the oil and set around your garden area will work. Hope that helps and good luck!
Sharon
Using the no till method, can you plant carrots in a container that just had beans or cucumbers? Will the old roots disintegrate quickly or will they get in the way of carrots?
Aaron (Mr. DeannaCat)
Hello Sharon, I think your carrots should be fine as the roots of those plants should be broken down by the time the carrots start to take form. A plant with a more extensive root ball could be more problematic such as a tomato plant. Thanks for reading and good luck!
Kim Babecki
Hi Deanna,
I’m so happy to have stumbled across your blog/website!!! I would love to actually take a walking tour through your garden!!!! Question … I have a large bag of ground organic sphagnum moss and I’m curious if you’ve found good uses for it or if you don’t use it at all.
Thanks for sharing your garden and knowledge with us!
Kim
Aaron (Mr. DeannaCat)
Hi Kim, thank you for checking out the site, it means a lot to us! As far as your large bag of sphagnum peat moss, you can work it into your garden beds or soil as an amendment. When using peat moss it is best to hydrate it before mixing it in, if used dry it can be hydrophobic and won’t absorb water. Hope that helps and good luck!
VIctoria
I have a a question in regards to your soil. I have watched a few of your videos and read a few of your articles, but do you just keep your extra made soil in a large trashcan or something for easy grab and go. I hate leaving half used bags of dirty, soil, compost, etc on the ground as I find when I water they tend to get wet and I worry about mold or whatever else could grow harmful in the sitting wet bag of soil.
This may seem like a fairly straightforward question but I know you have a good routine going and thought i’d ask.
Ps, Thanks for continuing to write educational and informative blogs. I find sometimes bloggers are strictly instagram now and its a bit short on the words to really get all the information that way.
DeannaCat
Hi Victoria – We mix our soil (so bagged soil, compost, bulk soil, lava rock etc) in place in the beds, so we don’t have extra “made” soil sitting around. If we have extra bags, we simply stack them outside under the overhang of the house (sealed). For the ones that are open, we roll the top up tightly and tucks it somewhere relatively dry too. Thanks for being here, reading, and for the nice comment!
Elizabeth L
I’m working on prepping beds for a fall/winter garden (zone 8b). I have a composted wood mulch from my summer garden on my in ground bed. I intend on using the no till method. What should I do with that mulch? Just leave it there and put the compost on top? Rake it out of the way and then place on top of the compost?
Thank you for all the advice you share! I’ve learned so much!
DeannaCat
Hi Elizabeth – It depends on the condition of the old mulch. We also often use a woody fine bark as mulch. Sometimes it is fairly broken down and/or decreased in thickness (the mulch layer) by the time we need to top the beds off, so we sort of just mix everything in right on top. We consider our compost topping part of our mulch layer. Yet if you have a pronounced thick layer of chunky mulch, I would push it aside, amend, and then put it back on top if possible. I hope that helps!
Patricia
Thanks for the response to the question of the mulch because I was wondering the same thing. You are my go to internet reading every day-thanks again for all the hard work you put in to providing this page!
Chris
We need some nitrogen in our garden. Will any of those fertilizers work for that?
I love your blog! I reference it daily!
Chris.
Tiffany
I have several raised beds, trying to grow mostly veggies in them zone 9b. I want to try and get a better soil mix for some new ones. How much mycorrhizae do you add to the soil when mixing. Also what do you recommend for reducing soil compaction. When it rains here in Florida it’s usually torrential and really compacts my soil
DeannaCat
Hi Tiffany – we usually add mycorrhizae to each planting hole (dusting the root ball of the new plant) or mix the powder with water, and water it in around the plant after planting – following the instructions/amounts on whatever brand we are using at the time. What are your raised beds filled with? It sounds like maybe they could use some more aeration materials for “fluff”? We like to fill our beds with a combination of some bulk soil, quality bagged soils (some made for container gardening/pots/raised beds that contain rice hulls, perlite or pumice to promote drainage and air) along with mixing in some very small 3/8″ lava rock for even more drainage and aeration. You can read more details about our soil mix and filling beds in this article. I hope that helps!
Kris
Your garden is beautiful. Thanks for the education. I typically garden pretty haphazardly. I am excited to use your tips and be more intentional