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
Katie
Hi Deanna, this is going to be my first summer trying no-till gardening in my raised veggie beds, after years of turning the soil every spring. I cut my plants down last fall and left the roots intact. I typically add plenty of mushroom compost every spring, but due to the current situation the only compost I’ve found in my area is cow manure (black kow). In your experience, planting seedlings and direct sowing seeds right into cow manure compost doesn’t impact growth or burn the plants? I know you said to keep them above the level of the soil additives, I just want to be sure that I don’t compromise my precious little seedlings 🙂 Thank you!
Johnny and Dani
We are so thankful to have stumbled upon your AMAZING website and IG!! We have poured over the majority of your posts and feel so much more equipped to tackle our new backyard! My wife and I live not to far from y’all, in Goleta (Santa Barbara County), and have taken this crazy shelter-in-place time to start our first (larger scale (by our terms) garden! We have 3 8×4″ raised beds that we filled based on your “perfect soil” article, and cannot wait to plant our veggie garden. We also live adjacent to a monarch butterfly preserve, so I can’t wait to get into your posts about those! So so cool, all that you and your husband do! Thank you for this information, you have truly inspired both of us!
DeannaCat
Hi Johnny and Dani – Small world! I’m glad you found us, and it sounds like you have some awesome projects in mind! Thank you for being here and for the kind comment. Stay safe and enjoy your home!
Nancy Krystek
Thank you so much for posting these informational articles! I truly appreciate the content you post here and on instagram, its one of the highlights everyday. I upgraded from containers and started my first raised garden two weeks ago and filled my beds with 50/50 compost and soil and planting mix which contains soil and some wood like chips which made me think I would have enough aeration. I’m finding my beds feel very compact and the water pools during watering which is making me believe I do not have enough aeration. I want to source some of the lava rock 3/8in like you suggested and I want to make sure I am buying the correct type, most of the options I see are for fire pits. Do you have a particular recommendation? I am also going to get some G&B soil conditioner like you suggest. Thanks for your help!
DeannaCat
Hi Nancy! We find our small lava rock at a local landscape supply company who also sells flagstone, bulk soil, etc. More of a contractor shop than a normal consumer big-box store. Do you have any companies like that near you that you could check with? If you can’t find it, I wouldn’t suggest the fireplace stuff if it comes in large chunks. Half-inch and bigger is too big. If you can’t find lava rock, pumice or perlite works well to – and also like I noted, many bagged soils already have those things (plus sometimes rice hulls) to create aeration. It is only reeeaaallly essential to add extra aeration if you’re buying bulk top soil and compost that has none at all. I’m not sure if yours was bulk, bagged, or had any of those items in it already? New soil can sometimes resist taking on new moisture. Try poking some holes in the top layer of soil and seeing if that helps it absorb more water? Once it gets wet and stays damp, it will usually draw it up easier. Mulching on top will also help retain and absorb moisture. I hope that helps!
Deirdre Davis
Forgot one more thing, seems like you grow a LOT of produce. I can’t imagine you can eat it all. What do you do with the extra? Besides preserving.
DeannaCat
Honestly, we don’t have that much leftover – after eating a ton fresh, preserving some, maybe giving some to the chickens. A small portion (if any) goes to compost on rare occasion. That said, we are vegetarian and eat a ridiculous amount of fresh produce. Ha!
Deirdre Davis
You mentioned you pull your out your whole tomato plants instead of just cutting the stem off. Do you recommend this in general or only if you have rot knot nematodes?
Also, you put you red wigglers in your beds? Thought it was not recommended to do that since they stay so close to the surface. I took a workshop before starting our worm bin and they had mentioned something like this. But wasn’t really clear on the why’s.
Thank you for the incredibly informative article. I printed out your garden planning kit and looking forward to using it. Love the companion guide! I have been needing one of these. No wonder our garlic and peas are not doing well. I had planted them together!
DeannaCat
Hey hey! So if you do not have nematode issues, you could definitely leave the tomatoes roots in place. It is up to you. And yes we add a few compost worms to the beds. They do stay fairly shallow, but certainly not just at the surface. When we do have a need to dig deeper into a bed (such as planting something) we regularly seem them 6-12 inches deep too, especially if it has been warm or the soil has dried out a little bit on top. They’re turning over organic matter and improving the soil for us. Even if they do most of their work near the surface, their poop is gold and welcome here – as it will get watered in and filtered down into the rest. That said, we add nightcrawler earth worms to the areas outside our raised beds (e.g. fruit tree areas, around perennials) for the very reason you mentioned. That way, those guys will dive deeper and do the good work where needed. I hope that makes sense! Thank you for being here, and for the kind words 🙂
Lindsay
Potentially stupid question: I use natural wood mulch. If I direct sow, should I remove that mulch?
Thank you!
DeannaCat
Not a dumb question! We usually wait to refresh the mulch the beds we are going to direct sow in, since seeds do prefer a finer fluffy soil to germinate in. If your mulch is already in place, try to move it aside in the spots you’re sowing seed if possible. Hopefully you don’t have to actually take it all out/off!
Jennifer
Perfect timing! I will be removing my summer garden and planting my fall garden tomorrow. Great tips.
Liz
Thanks Deanna! Really good info here. Appreaciate your hard work and thoroughness in all of your posts.
DeannaCat
Thank you for the feedback and support Liz! We’re glad you found it useful!
melly
Another timely article. This is my first fall garden. Why do gardens have to always be teaching us something? Can’t they just GROW?! 😂 Love your row-cover idea. Maybe I can grow brussel sprouts using this technique!
Thanks, Deanna!
DeannaCat
Oh come on, the constant challenges and learning moments are part of what makes it special! Lol. And the work – what makes it rewarding. Enjoy your first fall garden! You’ll be hooked. It is our favorite.
Michelle
Another fantastic blog post! I appreciate all of your knowledge so much! My winter garden is our project for the weekend and this came at the perfect time, thank you so much!!
DeannaCat
Excellent! So glad it came on time for you. I feared it was a little late for some folks… but better late than never! Have a great weekend playing in the dirt!