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Compost & Soil Health,  Getting Started,  Raised Garden Beds

How to Amend and Fertilize Garden Bed Soil Between Seasons

Last Updated on August 19, 2023

Out with the old, in with the new! In our garden, it is that time of year that we say goodbye to the fading summer crops and welcome in the new seedlings for fall. Are you curious about our garden “switch over” routine? Or, are you breaking ground and planting in a fresh garden bed for the first time? Let’s talk about how to amend your soil, either way!

Read along to learn how to prepare a new or established garden bed for planting. We’ll cover methods for removing old plants, a few words on no-till gardening, developing a planting schedule, how and when to amend soil, fertilizer selection, mulch, and more. Oh, don’t forget the compost! Always, compost. 

In a nutshell, we cut old plants out, add a few meal amendments along with a thick layer of compost to the top of the soil, plant the new seedlings, and finally top off with another layer of compost as mulch. Of course, there are many schools of thought on how to prepare beds and fertilize! We focus on feeding the soil, which in turn feeds the plants! The methods and products discussed below are simply what works for us, but I always encourage you to experiment and see what else may work for you too.

Ready to dig in? Great! Stay tuned for the time lapse video of us turning over a bed to amend soil last spring, at the end of this post.


When to plant or “turn over” a garden bed with new crops

Whether you’re starting fresh or planting a second round of crops, it is best to have some sort of planting schedule to follow. Seeds and seedlings like particular conditions to sprout, rapidly grow, or mature for harvest. Unfavorable conditions can set them back, or even kill them. This will vary by type of plant, time of year, and your climate! You likely already know this… Yet making that call of when is the “right time” to pull established plants to replace them with next seasons crops can be more tricky than it sounds! 

If you haven’t already done so, you can subscribe to our weekly newsletter and receive a free 20-page garden planning toolkit. It includes planting calendars for every zone! Even if you missed the window for starting seeds, don’t fret! Hopefully you still have time to plant some nursery seedlings instead. For more tips, see this article all about seed starting, and this guide on choosing the best seedlings at the nursery.

A planting calendar serves as a helpful guide, but deciding exactly when to plant or remove crops will ultimately come down to some personal judgement calls, and trial and error.  With time and experience, you’ll develop your own schedule for your particular garden, location, and crop preferences.

A planting calendar for Zone 10, it has many different vegetables lined up on the left side of the chart and all of the months of the year listed on the top of the chart. Each vegetable has different colored lines that correspond with when to start seeds inside, transplant outdoors, and plant seeds outside, along with corresponding last frost date and first frost date where applicable. The lines start left to right, showing what months you should do each particular task depending on the season and where you live.
An example of the planting calendars that are part of the Homestead and Chill subscriber garden planning toolkit. Calendars are included this for every USDA growing zone! Also included is a handy companion planting chart and plot plan template.

What about the plants that are still growing?

In order to start your next seasons garden at the “right time” – it may mean removing plants that aren’t completely finished producing yet! That is, unless you have ample garden space and free beds to start the newbies in while the old guys finish up. Or, if you aren’t planting anything immediately after. Then you can simply let them run their course.

For example, we always have to kill off many pepper and tomato plants that still have ripening fruit on them – in order to get our fall/winter greens and brassica seedlings planted on time. For us, this is at the end of September to early October. We have tried to wait a month later for the changeover, and the result was our saddest winter garden to date! Those few additional tomatoes and peppers were NOT worth the expense of a floundering winter garden.

In the fall, if you wait too late plant seedlings or sow seeds, the crops may fail to thrive due to the reduced sunlight hours that the shortening days bring. Getting them started while the soil is still warm and the sun is shining for most of the day will give them a great jump start before the shorter, colder days come. This is true even for places with temperate frost-free winters. 

On the flip side, allowing the surviving winter crops to grow long into spring isn’t always the most fruitful either. Especially if you have the opportunity to replace them with fresh productive plants, or get a jump start on your summer garden! As the days begin to lengthen once again, it often triggers greens or brassicas that have survived over winter to begin to bolt or flower. 

A three part image collage, the first image shows a number of garden beds, most of them are full of mature plants that are still producing fruit. There are various pollinator plants planted throughout the area as well. The second image shows the same garden beds, however, all of them are now empty except one. There are soaker hoses sitting in two of the three beds and some of the soil looks disturbed from removing the plants. The third image shows the same garden beds after being re-amended with fertilizer and fresh compost. The garden beds have also been planted out with tender young seedlings, spaced in neat rows, all standing up perky, pointing towards the sun.
When we remove older plants, be it during the fall or spring, we almost always have to kill plants that still have some producing-potential. But oh, the fresh start is worth it! In the fall and winter months we grow broccoli, cauliflower, cabbage, kale, mustard greens, bok choy, lettuce, arugula, swiss chard, and more! We will also direct-sow fava beans, garlic, carrots, radishes, and beets very soon.


When it is time to remove old plants from a garden bed, we prefer to cut them down like a tree at the soil line or just below, rather than pulling up the whole plant by its roots. Thus, the roots are left behind in the soil. This is called “no till” or “no dig” – a gardening philosophy that we mostly follow, though not strictly. If the spent plants aren’t diseased, they are added the compost pile – or fed to the chickens, when edible and appropriate. Otherwise, they go in the green waste.

Why leave the plant roots in place? 

When roots are removed and the soil is therefore disturbed, all of the beneficial microbial, fungal, and mycorrhizal associations that have formed are disrupted too! Soil is a living thing, after all. We have worked hard to create those networks of happy microbes by inoculating our soil with worm castings, worms, compost tea, mycorrhizae, and beneficial nematodes over the years. Think about a natural environment, like a forest floor. Is it manually tilled? No. The soil structure is left intact while the critters do their good work down there. 

No-till farming reportedly increases soil biological diversity, fertility, resiliency, water retention, organic matter, & nutrient cycling. In contrast, tilling soil increases erosion and disrupts beneficial life underground. The roots left in place to decompose in a no-till system will break down over time, providing food and nutrients to the worms, microorganisms, and other detritus-eaters in the soil – which in turn feeds the plants. 

Check out Uncle Jim’s Worm Farm to get worms for your garden! We add red compost worms to our raised beds (and worm compost bin), along with European night crawlers to the areas of our yard with fruit trees and shrubs – because they like to dive a little deeper.

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 away old broccoli and cauliflower stems, using a small saw to cut the dense stalks at the soil line.

When tilling soil can help

I mentioned that we mostly follow a no-till philosophy, but we aren’t total sticklers about it. There is certainly a time and place when things could use a fluff. Particularly if you’re just getting started and need to amend soil in a new garden bed. Also when an established bed seems overly compact and needs fresh compost or aeration material worked in more deeply, such as the small ⅜” volcanic rock we add to our beds. In lieu of tilling, the addition of worms can help to increase aeration naturally!

Another time when a no-till method may not be preferable is in soil with a known infestation of root-knot nematodes. These are microscopic pests that feed on roots, causing tell-tale nodules and sometimes stunted or unhealthy plants. Removing infected roots, tilling, and exposing the nematodes to air are ways to reduce their population. However, they’re hard to battle with that alone! Even when we attempted to fully till a bed to reduce their populations in the past, they were still present the following season. 

One organic method we use to reduce root-knot nematodes (which we have a very minor/occasional issue with) is applying these beneficial nematodes to the soil – who act as parasites to overpower the pest nematode populations, along with cut worms, root maggots, grubs, fungus knat larvae, and more! In combination with removing obviously infected roots (mostly tomatoes and squash), that stuff is pretty effective for us! Now we do remove our tomato plant roots, but do not till the soil, and the signs of root knot nematodes have been decreasing!

A hand is outstretched with the palm facing upwards. A stem of a plant is nearby with its roots exposed, the roots are bulbous and knotty with many irregularities. These roots have been affected by root knot nematodes.
Roots infected with root knot nematodes.


Preparing a new garden bed for planting

For a brand new raised garden bed, you may not need to do much in the way of adding fertilizer – depending on what you filled the raised bed with, that is. If you happened to follow our suggestions for filling a raised bed, which includes adding quality soil, a lot of well-aged compost and a small amount of mild fertilizers from the start – you’re good to grow! 

However, if you filled your garden bed with native soil and/or your average bagged potting soil alone, the soil and future crops will appreciate a little amending! In that case, follow the instructions below for fertilizing established beds below. The same goes for in-ground gardens, old and new. Aside from the practices to follow, there are only a few extra amendments we add to new beds, such as basalt rock dust. 

How to amend soil in an established garden bed for a new round of plants

As plants grow, they continue to draw up and use nutrients from the soil. Depending on how rich the soil is or how hungry that plant was, the soil could be left pretty depleted after a growing season! Therefore, we need to replenish lost nutrients in order for future plants to happily grow.

After clearing the old plants away, we top off our raised garden beds with amendments and a nice thick layer of compost. In terms of amendments, we prefer to use mild, slow-release, organic fertilizers such as kelp meal, alfalfa meal, crab meal, and neem seed meal. Or, instead of a combination of many, gardeners may apply one well-balanced all-purpose fertilizer.

How to apply dry “meal” fertilizer to garden beds

To apply meal-type dry fertilizer to a garden bed, simply sprinkle it evenly across the soil surface. Then, work it into the top few inches of soil with your fingers. I recommend wearing gloves! To determine the amount of fertilizer to use, follow the instructions on the package per square footage or surface area you are amending. However, I suggest going on the light side of the recommended application amounts! After application, water the soil to allow the fertilizer to begin to seep it. It will continue to break down and release nutrients with time.

Note that all of the fertilizers we use are fairly low in their nitrogen, phosphorus, and potassium ratios – also known as NPK. Our goal is to give the plants a small boost of those key nutrients to get started, but not overpower them with such strong fertilizer that it could potentially shock or “burn” the young seedlings. The added compost, existing soil, and worms will feed them essential micronutrients and minerals too! There is a lot more to healthy plants than just NPK.

A three part image collage, the first image shows a garden bed that is empty of plants yet is full of soil. There  is a whitish dust spread throughout the top of the soil. There is a wheel barrow next to the garden bed, as well as various marigolds. The second image shows a blue bucket sitting on top of an empty garden bed, a hand is holding a measuring cup of sorts directly above the bucket where the measuring cup and bucket both contain various amendments used to feed the soil and the plants that will soon be planted in it. The third image shows the top of a garden bed, the soil has been sprinkled with the amendments, and a gloved hand is starting to scratch the amendments into the soil, mixing it into the top inch or so.
Follow instructions on the package (on the light side), sprinkle it evenly over the soil surface, and use your hands to scratch the fertilizer into the top few inches of soil.

Our gentle fertilizing methods reduce the risk of shocking young plants, and also reduces the complication in tailoring the soil to particular plants. We treat the soil in all of our raised beds essentially the same from the start. Then, we can later give heavy-feeding plants additional food throughout the growing season as needed with aerated compost tea, dilute seaweed extract, or alfalfa meal tea. We can also do another round of top-dressing of meal fertilizer and/or compost in a few months if needed.

It is easier to add more food than take it away! For example, if you hit your beds with a ton of high-nitrogen fertilizer right from the start, not only do you risk burning seedlings – but you may also piss off some other plants for the whole season. Leafy greens such as kale and cabbage may love all that nitrogen, while other crops like carrots or radishes don’t like excess nitrogen – and will not develop as well. 

When to amend soil 

It is best to amend soil close to planting time. In mild climates with extended or year-round growing seasons like ours, we amend the soil in our garden beds twice per year – in spring and fall. Ideally, add fertilizer a week or two prior to planting. That way, you can water it in a few times and allow it to mellow out before the plants go in. This is especially true if you’re applying more “intense” fertilizers than we use. However, due to our tight planting windows, we don’t always follow this advice…. We are guilty of fertilizing directly before planting seedlings, but they don’t seem to mind! 

For folks with harsh freezing winters, or who are otherwise choosing not to garden over the winter – wait until spring to amend the soil. If you apply fertilizer in the fall and leave the beds empty, rain will just wash away much of the added nutrients.

Preparing garden beds for winter

If you plan to allow your garden beds to lay fallow (rest) for the winter, start by clearing the old plants. Then, apply a fresh thick layer of mulch. We’ll talk more about mulch options in a moment! Furthermore, you could throw down some cover crop seed and allow that to grow while it can. 

Cover crops provide mulch, reduce erosion, and also naturally amend soil by fixing nitrogen – drawing it into the soil by their roots. Good nitrogen-fixing cover crops include fava beans, peas, clover, vetch, lentil, flax, and more. Check out this great cover crop seed mix! At the end of their growing season, allow the cover crops to either fade in place, or cut them down and leave the plants on top of the soil. This practice is known as “chop and drop” mulching. The nutrient-dense plants will decompose in place and feed the soil. You could also clear and add the cover crop foliage to your compost pile. Either way, leave those roots in place!

Ultimately, you can grow cover crops to rejuvenate otherwise resting garden beds at any time of year, not just during winter! While we don’t usually allow our beds to full-on fallow. Yet we do periodically rotate nitrogen-fixing crops like fava beans and green beans among our beds to help amend the soil. We also “chop and drop” or green mulch with other biodynamic accumulators like comfrey and borage throughout the year. I love feeding plants with plants.

A u-shaped garden bed next to the side of a house is lush with growing greens, brassicas, and legumes. There are mature red cabbage heads, carrot greens, mustard greens, and asian greens. Behind the red cabbage there are many flowering fava bean plants shooting upwards towards the sky. They come up to the bottom of a window in the image. There are four curious chickens at the foot of the beds, looking upwards at the vegetables that they may be able to consume. There is a sign of the house that says "garden" and there are various trees and pollinator perennials beyond the edge of the house.
A nice chunk of fava beans planted among our other winter crops. Sometimes, we plant an entire bed of favas. They are excellent nitrogen fixers, in addition to providing edible beans – and greens! I am working on a post all about growing fava beans next. Stay tuned!


After dusting our garden beds with meal fertilizers and working those in, we top the soil off with a couple inches of well-aged compost. We add an inch or two before we plant things, lightly mixed into the very top layer of soil. Then we add a final inch or two of compost as mulch, after planting the seedlings.

As much as possible, we add homemade compost and worm castings. Unfortunately, we can’t make quite enough homemade compost to meet all our compost needs. We currently have 15 raised beds and several wine barrels to prepare for a new season, after all! Therefore, we mix our compost with a few favorite bagged compost products. Malibu’s compost is one go-to, made from certified organic dairy cow manure and biodynamic accumulating plants. We usually lay Bu’s down first with the amendments, lightly worked into the soil, because it is finer and richer. Then, we top off with a more coarse Gardener and Bloome “soil building conditioner” as the final mulch layer after planting. 

In regards to compost options, seek out what you can find locally! Some landscape supply companies sell pretty decent compost products in bulk. 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. Organic is all the better. Heed caution with mushroom compost to amend soil. While rich in nutrients, this study shows that it has the potential to kill germinating seeds.

Two raised garden beds are shown, they have been cleared off all old plants and have fresh compost spread over the top of them in a pile. The compost is Bu's Blend Biodynamic Compost and it will soon be spread evenly over the entire surface of each of the garden beds. One of the bags of compost is laid out on one of the beds and compost to show the brand of the compost. The background contains lush perennials with pink flowers, cacti, flowering basil, and part of a tomato plant.

Boom! Your soil is now dressed to the nines, ready for some new plant babes to come jump in bed.


It’s time to get those seedlings in the ground! Or, to direct-sow seeds. Check out our in-depth guide on transplanting best practices here, which covers important concepts like hardening off, plant spacing and depth, and whether to loosen the root ball or not. Then, this article explores when it’s best to direct sow seeds (e.g. root veggies, always!) versus the benefits of starting indoors or transplanting seedlings.

Come planting time, we add a few more goodies to the soil. Every planting hole gets a little handful of worm castings from our our worm bin (or, you can buy worm castings here). Worm castings have been dubbed “black gold” for plants for a reason! They’re loaded with nutrients and beneficial microbes, but are incredibly gentle and slow release – posing zero risk of burning your tender seedlings.

We also add a sprinkle of mycorrhizae (a beneficial fungi) around each root ball. Mycorrhizae increases root growth, nutrient uptake, and disease and drought resistance! It can also help lessen transplant shock. Learn more about the vast benefits of mycorrhizae here.

A little handful of worm castings goes in each planting hole to provide immediate but gentle nutrients.


After planting seedlings, be sure to mulch the top of your soil! About 2 to 4 inches of mulch is ideal. The finer the material, the more effective it is at moisture retention and thus less is needed.

Mulch helps plants and amends soil in numerous ways. It improves moisture retention, keeps worms and microbes happy, prevents erosion, acts as insulation to reduce temperature swings to soil and plants roots, reduces “crusting” of the top soil and related water runoff, breaks down to feed the soil, slows weed growth, and keeps things looking spiffy!

As I mentioned, we use compost or compost-like products for mulch – added on top of our BPA-free drinking-water grade soaker hoses. Other mulch options include leaves or leaf mould, straw, cane sugar mulch, wood chips, finer bark products, pine needles, grass clippings, and more. Use what is readily available to you locally! If you do opt for straw, I highly suggest seeking out straw that doesn’t contain seeds. Otherwise, it can sprout and create a weedy mess.

Read more about the pros and cons of 8 popular types of mulch here.

A raised garden bed is shown after it has been amended and planted with fresh tender seedlings. The seedlings are lined up three wide and six deep and there is a soaker hose snaking its way back and forth the length of the bed, passing by each seedling. Fresh compost will be added to the top of this to act as mulch and to cover the soaker hose. There are a couple garden beds in the background that still contain mature plants that are flowing over the edges of the beds. They will soon be removed and the beds will be teated in a similar manner as the newly planted one.
After planting and watering, before mulch is added.
Four raised garden beds are shown, three of which have been recently amended, planted with fresh seedlings, and mulched with compost. The seedlings are in neat rows and are standing straight up towards the sun, showing that they are happy in their new home. The fourth garden bed still contains mature plants that will soon be gotten rid of and the bed will be treated in a similar manner as the other three. The background is a green wall of flowering salvia, sage, cacti, small trees, and passion fruit vines.
After adding mulch to cover the soak and soaker hoses.


After transplanting, provide your new seedlings (or sprouting seeds) some protection if needed. There is nothing worse than going through all that effort and then having something damage or kill your plants! Trust me. Been there, done that. We have an issue with wild birds picking at our smallest tender seedlings here. Therefore, we add these awesome little hoops with netting on top to keep them safe until they get larger and more established!

The row cover netting we use is dual-purpose, and also keeps cabbage moths and other flying insects away. A similar set-up can be used with a thicker row cover meant for frost protection, if that is a concern where you live. This may also help to deter squirrels, rodents, cats, and other larger pests – unless they’re really determined! Learn all about using hoops and row covers for pest control, shade and frost protection in this article. It also covers how to set up DIY PVC hoops and various row cover materials.

Numerous raised garden beds are shown with green gravel rock surrounding them. Three of the beds have been recently planted with fresh and tender seedlings, hoops have been erected over the beds and white insect netting has been clipped to the hoops, enclosing the inside of the beds to birds and pests from the outside. The other garden beds still contain bigger and more mature plants that are nearing the end of their life as the season has started to change. The background contains flowering basil, guava shrubs, magenta bougainvillea, lavender, salvia, zinnias, and numerous other trees, annuals, and perennials.
Protecting all our newly planted seedlings. In these beds are many types of cauliflower, kale, mustard greens, bok choy, and various other asian greens. Now to turn over the remaining beds!

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! If you’re here reading this, I assume you already have a garden set up? Yet if you need any tips on how to design and build raised beds, check out this article.

Always feel free to reach out in the comments with questions, feedback, or just to say hi. Let us know what’s going on in your garden, or what types of mulch or compost you like to use! Also feel free to share this article with your friends, or pin it below. Thanks for tuning in, and happy planting!

Us, turning over a garden bed no-till style between the old winter crop and new summer crops. This bed was already really full or we would’ve added even more compost on top!

DeannaCat signature, keep on growing


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