Problems with Raised Bed Soil: How to Troubleshoot and Revive a Raised Garden Bed

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Have you ever suspected that something wasn’t “quite right” with your raised bed soil? Perhaps your plants didn’t grow as well as you anticipated. That’s usually the first indication something is amiss.

As I’ve observed different raised bed soil mixes in my own garden, I have seen first-hand just how important soil quality is. The differences between plants grown in healthy soil and so-so soil (or outright terrible soil) are quite noticeable.

If you’re looking to troubleshoot your raised bed soil, I’ll share what I believe to be the most common culprits of poorly-performing soil. Click below to listen to a full and detailed explanation in this episode of the Beginner’s Garden Podcast, or continue reading for the main points.

First of all, let me be clear. I am neither a soil scientist nor an expert on this topic. I am, however, a seasoned gardener of eight years and I’ve tested different soil combinations. Because of this, I have a few ideas and have done the research on what good, healthy soil is.

gardener near raised bed
Some of my raised beds are more productive than others, and I can always point to a difference in the quality of the soil.

What is Good Garden Soil?

Before we can understand what’s going wrong with a raised bed soil combination, we need a proper understanding of what makes up good raised bed soil — balanced texture, proper structure, adequate organic matter, and active soil organisms.


If you’re like me, maybe you only think about dirt and nutrients when you first think about the garden soil, but what you need to be thinking about first is texture. Texture is defined as the relative proportion of sand, silt, and clay. Each of these soil textures has different particle sizes. A mixture of them all — loam — is ideal.

loam soil
A healthy soil consists of a “loam” mixture of sand, silt, and clay.

Sandy soil is made up of the largest soil particles. It makes water much easier to drain but often it drains too fast. Sandy soil also doesn’t retain nutrients well, making it harder for your plants to thrive.

Clay soil is made up of the smallest soil particles, causing them to stick together closely. This impedes proper drainage. The roots of plants need oxygen to thrive and when our soil is so closely compacted with thick clay, the roots suffocate. But clay isn’t without its benefits. With clay soil, you’ll often find high nutrient content.

Silt falls somewhere in the middle of the two and has more of a smooth or floury texture.

Good garden soil is a combination of all three. Clay helps provide nutrients and good water retention, and sand helps aerate the soil and balance with good drainage.


Texture is just one quality of good soil. Soil structure is another. Soil structure is defined as how soil holds together.

The best way to determine the soil structure in your garden is to pick up a handful of soil that’s a little bit damp and make a fist. If it just stays in a shape and doesn’t crumble, it’s probably too much structure. If it doesn’t hold any shape at all, it’s too loose. It needs to be somewhere in the middle.

ideal soil structure
Organic matter “glues” soil and creates proper structure.

The way to get good soil structure is organic matter, which is considered the “glue” that holds the soil together.

Organic Matter

Soil organic matter is basically something that used to be alive that is starting to break down. Most quality garden soils consist of only 3% to 6% of organic matter. So don’t feel like you need to have a bed full of organic matter to have good soil.

To explain how organic matter behaves in your soil, you need to understand its decomposition process. This happens in a compost pile but it also happens as any organic matter goes from fresh material to a stable, decomposed material (and everything in between).

Compost pile
You can see the stages of organic matter breakdown in these two compost piles — the one on the left has fresh organic matter; the one on the right has been composting down for a period of time.

In stage 1, soil microorganisms begin to break down fresh organic material.

In stage 2, the decomposition of this fresh material is ongoing. This simply means that the organic matter you’ve added to your garden soil is in the process of breaking down, again, by the action of soil microorganisms.

During this process — both in stages 1 and 2, nutrients are being released — due to the action of soil microorganisms — for plants to use.

In stage 3, the organic material has broken down to a point where it is known as stable soil organic matter, better known to most as humus. Humus is the ideal stage because the organic matter isn’t breaking down anymore, so this provides a good soil structure.

In an ideal raised bed soil, organic matter is passing through all three stages at once. For more information on each stage and the critical role humus plays in your soil, this publication from Cornell University explains it well.

putting compost on garden during the fall

Soil Organisms

You may have noticed a theme in the decomposition of organic matter — soil microorganisms.

In order for the plants to take up the nutrients in a way that it can use, organic matter is dependent on soil organisms to make that nutrition available for the plant.

Soil organisms could be things you see like earthworms or their castings. Other organisms are fungi or good bacteria that you can’t see but are doing their work below.

Without organic matter, soil organisms have little to “feed” on, which means your soil will have little nutrition. In turn, the soil won’t have a healthy blend of humus that’s necessary for so many functions of the soil.

That’s why both organic matter AND soil organisms are so important to our plants.

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How do we Support Soil Organisms?

If we know that soil organisms are so important, how to we support them in our raised bed soils?

First, create an environment for soil organisms to thrive. Work to make the soil well-aerated, well-drained, and moist. This goes back to making sure our soil texture and structure is right. We want to make sure our soil doesn’t fall apart but it doesn’t stick together, either.

Second, correct any extreme pH issues. Most gardens grow best with a pH of 6.0-7.0. Some plants can tolerate less than 6.0 (blueberries must have less), but for the most part, the majority of gardens will fall in that range. When you have an extreme pH, your soil organisms will have a harder time.

How do you know what your pH level is? You’ll need to test your soil. For an easy option, I recommend SoilKit. You can use home tests, but if you want something specific, we definitely recommend sending it to a lab.

The next thing you can do to support your soil is to steer clear of non-organic pesticides and I even recommend using organic pesticides in moderation. Another benefit of your organic matter is that its presence helps decompose some of the chemicals in pesticides, but still, use care.

Along that same line, don’t use synthetic fertilizers. These can upset the natural chemical balance of your soil, which can impact your soil organisms. There is conflicting research out there on this, but for me as an organic gardener, it’s just not worth taking the chance.

The final thing you can do to support your soil organisms is to continue adding organic matter. This allows organisms to continually feed. If you want to go a little bit further, try and keep something growing in your garden at all times (like cover crops). This allows good fungi and bacteria to grow and thrive on plant roots.

compost - way to save money gardening

Four Causes of Unproductive Raised Bed Soil

Now that you understand the workings of good raised bed soil, what could be causing issues in your present soil?

The first is the lack of soil organisms. Remember, it’s the activity of soil microorganisms that allow organic matter to break down and release nutrients that the plants in your garden can use. When plants don’t have a way of uptaking nutrients, they can’t thrive.

The second possible cause of an unproductive raised bed is that organic fertilizers are slower to release their nutrients. For example, blood meal takes two to six weeks to begin releasing its nutrients. Some organic fertilizers — like bone meal or rock phosphate — can take months to become available to the plants. This isn’t a bad thing — the slow-release action of these organic fertilizers will provide for your plants in the long-term, but if you’re seeing slow growth at the beginning, it could be that your plants aren’t getting these nutrients just yet.

The third probable cause in poorly performing raised beds is what I think caused poor results in one of my three raised bed soil tests. If you have used 100% bagged soil, it’s possible the high concentration of bark products in your raised bed soil mix has “robbed” nitrogen from the plants if the bark hasn’t been fully composted. When we add fresh wood into our soil, it uses nitrogen in the soil to break the wood down, thus temporarily robbing our plants of their nitrogen. In my case, over time, my soil settled once those bark products reached stage 3 (fully broken down) and it now produces at the rate that my other beds do.

bagged garden soil for tomatoes
This bagged soil blend had lots of bark content that I believe robbed nitrogen from these young tomato plants.

The last potential cause of raised bed soil issues is an out of balance pH. I don’t think this one is as big of an issue when it comes to the bagged soils you buy. But, if you’re bringing in native soil from your own property, you may want to consider a soil test.

What are My Best Performing Raised Beds?

Now that we’ve talked about healthy soil and looked at possible causes of poorly performing raised bed soil, you may be asking what IS the best combination of raised bed soil? I continue to test, and this guide will help you evaluate your options. But in my garden, here’s what I’ve found to be my best performing raised bed soil combination:

My best performing raised beds have been a combination of topsoil and compost. I’ve used native soil from my own property and topsoil from a reputable local nursery, and both have performed well, though I’d say my native soil performed the best. For compost, while I do make my own compost, I don’t make enough, and I’ve found a high-quality source of compost in my local area that has performed well year after year in every bed I’ve used it.

Bulk Compost from Garden Center

I know that not everyone can buy in bulk or justify the cost of buying in bulk. So, then, what do you do? I would suggest a bagged soil that has a good reputation. In my personal experience, I’ve had trouble finding that at big boxed stores. I definitely suggest going to your local nursery and asking local gardeners what they have found to work the best for them.

Second, consider your soil organisms. Start, right now, with composting. Winter is the perfect time to get your compost pile going. It’s easier than you may think and adding your own compost will help more than you might ever think it would.

A healthy raised bed soil with good texture, structure, balance of organic matter, and active soil microorganisms is the best quality raised bed soil you can build.


  1. I realize that as a “blogger”, “podcaster”, publisher, etc. it may be unwise to recommend certain products by name. However, it also seems that leaving the choices to your audience also may introduce some errors in building the correct soil texture, structure and organically correct raised bed soil. I would love to know for the hobbyist gardener specific names of things you would recommend.

    1. Hi Tim, I don’t have any problem sharing great experiences with great products. In this particular instance, however, I have not personally had a good experience with bagged soil for raised beds. (I also have not tried many kinds because I have found my best experience in bulk soil and compost.) I have had excellent results from ProMix soil with seed starting and containers. As far as brands for bagged soil, I asked the members of my Facebook group to share their good experiences and the most common brands (organic) that came up in that discussion were: Soil3, Miracle Gro Organic Soil, and blends from Fox Farm. (I have used Fox Farm mixes with my seed starting with good results.) In the podcast episode that this blog post was based on, I go into more detail on my personal experience with bagged soil in general and some general recommendations, so you might find it helpful to listen (it’s linked at the top of the blog post).

  2. Hi Jill. Larry from Washington state here. Do you have a percentage of compost to top soil that you prefer? We have a terrific source of compost from our local landfill. It’s relatively inexpensive so I can buy it by the yard.

    1. In my experience, the ratio is relatively fluid. I did a 50/50 blend last year and had great results. I’ve also done 50% topsoil, 30% compost, and 20% other materials. It probably also depends on the quality of topsoil. My bulk topsoil source is heavy on clay and silt so that’s why I think the higher ratio of compost helps that. For a more typical topsoil, you may not need as much compost.

  3. I loved your podcast, “What is Wrong with My Raised Bed Soil”! I especially loved the end of the podcast when you shared scripture and talked about being stewards of the earth and what God has given us. I am a believer as well and have a personal relationship with Jesus Christ. I am concerned about the health of our soil as you are. I hope to put in some raised beds before Spring in order to grow more produce this year. I have seeds ready to go. Our soil on our property is totally depleted of organic matter and microorganisms since this area was once used for cotton crops. I appreciate the good information that you shared!

    1. Thank you, Pam! I think raised beds are a great option for the soil you have. Eventually, I suspect the soil would recover with some care, but raised beds will get you a better harvest, quicker.

  4. I just found your blog when looking for answers for one of my raised beds in which plants for the last 3 seasons have not been able to grow more than a couple inches and then turn yellow. I’ve added bone meal which was indicated by a soil test and waited a few months, but the new planting was the same. Today I dug down and found thousands of tiny roots, very dense and compact throughout the first 8 inches of soil in that bed. No trees are nearby and the roots are super fine and white. Any suggestions? Thanks for any help. I’m also going to look up your podcast!

    1. That almost sounds like a good fungal growth that you want in your garden. But not seeing it, I can’t be sure. Look up mycorrhizae to see if it might be that.

  5. Hi. I have a few questions. These are great reads and I’m starting to understand what might be wrong in our beds. But how much stuff do you add if the beds are already filled pretty much all the way? The depth of soil is 9″ and 1″ of mulch on top with just 1″ of remainder room till the top of the bed. I know that I want to add worm castings and compost but how do I calculate how many bags of each will go in and how much soil I have to take out to make room? Any ideas on what to do with the soil that I will need to remove? Or if not removing any of the current stuff in the bed, how much will I be able to practically wiggle in there without overflowing? My beds are 4’x4’x11″.

    1. Here’s a soil calculator to help with knowing how many bags to buy:
      For your other questions, if you’re just needing to amend with better soil, you can take out as much as you think you need to. For good garden soil that just needs a refresh, 1-2″ of compost on top (remove the mulch first) is sufficient. But if you think there’s more going on with the soil, you could remove half or even all. A soil test would help in knowing if there are significant issues. If your soil isn’t contaminated, I’d just put it in a pile and use it in a mix to refresh the soil in the future, along with new compost.

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