What Is Organic Fertilizer?

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Robert Pavlis

If you read a number of web sites, especially organic gardening ones, you quickly realize that there are two basic kinds of fertilizer. There is the ‘synthetic fertilizer’ which you buy in bags. This fertilizer is clearly BAD! Then there is the good stuff; organic fertilizer.

What is the real difference between organic fertilizer and synthetic fertilizer? Is there a difference? The answer may surprise you.

variegated Lilly of the valley
Variegated Lilly of the Valley – by Robert Pavlis

What is Fertilizer?

Wikipedia defines fertilizer as any organic or inorganic material of natural or synthetic origin (other than liming material) that is added to a soil to supply one or more plant nutrients essential to the growth of plants. From a gardeners perspective, fertilizer may contain NPK and minor nutrients (sulfur, magnesium, iron etc). The NPK number is a short form for nitrogen, phosphorous and potassium.

Synthetic Fertilizer

Synthetic fertilizer is also called inorganic fertilizer or commercial fertilizer to differentiate it from organic fertilizer. This fertilizer is either mined from the ground or synthesized by man. It consists of granular material and comes in bags.

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Organic Fertilizer

Any fertilizer that originates from an organic source is considered to be organic. Some examples include fish extracts, bat guano, manure, and compost. It can be purchased in bags or bottles and can be ordered in bulk as trailer loads.

What Does the Plant Need?

To better understand the differences between fertilizers it is important to understand things from the plants point of view. What nutrients can a plant use? Can it distinguish between a synthetic and an organic source?

Plants get almost all nutrients through their roots. You can think of the outside wall of the root as having small holes or pores. These holes are used to let certain molecules into the root. The process is more complex than this, but it is not a bad analogy.

These holes are quite small and so only small molecules can get through them. Water molecules consisting of H2O are small enough and get into the root. Nitrate is also a small molecule, NO3, and it is also absorbed into the root. Other nutrients such as phosphorous, potassium, iron, magnesium etc are all small enough to enter the roots.

Large molecules like proteins, DNA, carbohydrates etc are huge in size compared to the nutrients. They just don’t fit through the holes. In fact most organic molecules fall into this category.Plants can’t use most organic molecules found in the soil! Almost all of the organic material in compost, manure etc is of little use to plants – they simply can’t get the molecules into the roots.

Large organic molecules do contain nitrogen, phosphorous, potassium, iron, for example, but in the organic form they are too big to get into the roots. For example, protein is a good source of iron, but because protein molecules are so big, plants can not use the iron contained in the protein.

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Eventually these large organic molecules do break down and when they do, the small nutrient molecules are released, and then plants can use them. For a better understanding of this see Compost – What is Compost.

Plants need the small molecules in order to grow. One of the key nutrients, besides water, is nitrogen and plants usually get nitrogen in the form of a nitrate molecule.

Synthetic and Organic Nitrate Molecules

Let’s look at nitrate molecules in more detail. What is the difference between a nitrate molecule from a synthetic fertilizer and an organic fertilizer? The pictures below shows the two molecules.

nitrate molecule

nitrate molecule

         Synthetic nitrate molecule                                                              Organic nitrate molecule

 Can you see the difference??

There is no difference. A nitrate molecule from either source is exactly the same. More importantly plants can’t tell the difference either.

I’ll repeat the last sentence since it is one of the biggest gardening myths. There is absolutely no difference between a nitrate molecule from a synthetic source and a nitrate molecule from an organic source.

This last fact is hard for the pro organic movement to believe. How can they be the same when organic is so much better?? The fact is that when it comes to providing nutrients for the plants, organic is NOT better. It is exactly the same as a synthetic source.

Is Organic Fertilizer Better?

From a strictly chemical nutrient point of view organic is not better, nor is it worse than synthetic. It is exactly the same. However we can look at things from a different perspective and then we will find that organic is better- see Organic Fertilizer – What is it’s Real Value?, for more details.

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Robert Pavlis

I have been gardening my whole life and have a science background. Besides writing and speaking about gardening, I own and operate a 6 acre private garden called Aspen Grove Gardens which now has over 3,000 perennials, grasses, shrubs and trees. Yes--I am a plantaholic!

21 thoughts on “What Is Organic Fertilizer?”

  1. Thanks for sharing this information with us by blog so that people can better understand the Organic fertilizers Options available in the market and get the proper benefits in their gardens. Thanks again

  2. Just to clarify: you state that synthetic fertilizer is chemically the same ionically as organic.

    Just out of curiousity is it the same exact chemical structure? For instance, there are synthetic street drugs where the molecular formula is the same but thg here is a slight change in the bonding which appears to have a great effect on the user which is not the same as the original drug. It’s a slight change which allows the synthetic(at least in the past) to be sold legally for a short time.

    I’m curious bc I have not researched it if the chemical l structure is exactly the same.

    I have an open mind snd I know science. I also do not portend ultimate knowledge. I also know humans(being one I am also culpable in this), create narratives. How much bias are you carrying and why?

    I’m not looking to put you or anyone down, I am merely in search of the ever elusive truth. I don’t buy everything permaculture sells but I don’t disregard it either. I have read some of the books that the design manual references who are done by orher scientists but as the manual is, are much older(though it does not mean incorrect). I have grown many plants and animals for years. I too have found nature knows what it wants. One thing I found was many plants where I live hate direct sun in the summer here. I can grow those under heavy partial shade and they thrive.

    Enjoying reading your book and the intellectual challenges it provides me, so that I can reexamine and untangle my own personal biases.

    • I never said ” synthetic fertilizer is chemically the same ionically as organic.” I might have said that the nitrate molecule from both sources is identical. They are absolutely identical on a molecular basis.

  3. Extremely useful and subcategorized information of organic fertilizers described in this blog.

    Thanks for sharing this blog with us.

  4. I see a lot about them being the same, yet little talk about the major differences in nutrient uptake process. Synthetic Nitrates and Ammonium Salts have to be in the proper PH range for a plant to most effectively absorb them. Organic fertilizers are broken down over time and transferred via cations and anions at the plant’s root zone. Soluble fertilizers are directly uptaken when ph is correct, and then broken down by the plant.

    There are plenty of scholarly studies that suggest organics are better for long term soil health. Here’s one.


    Plus, synthetics used irresponsibly can have some really bad consequences. Sure there can be some of the same effects with irresponsible organics, but is there any evidence like this?


    I’m curious if there is any quality academic literature to support your argument? Do you believe that long term applications of the two methods have the same effect on soils?

    To equate the two methods because they have the same chemical structure is a false equivalency.

    Sure there are advantages to synthetics. They are cheaper, the yields are better, and they require less material. But on the other hand, over application can result in negative effects such as leaching, pollution of water resources, destruction of micro-organisms and insects, crop susceptibility to disease attack, acidification or alkalization of the soil or reduction in soil fertility — thus causing irreparable damage to the overall system. It can lead to softening of the plant tissue causing more pest and mold susceptible plants. Also, organic fertilizers are superior for AM fungal life in the soil.


    One of these two process is proven to have catastrophic environmental effects when improperly managed. One of these two processes is proven to create a more diverse fungal network in the soil. One of these two processes evolved naturally over millions of years. One of the processes leads to a superior end product.


    If there was more real academic evidence to suggest that long term responsible synthetic farming practices and long term responsible organic practices were completely equal in their environmental effects and end product quality, I might be a little more compelled by this blog post. As of now all I see are pictures of nitrate and not a single piece of noteworthy academic research that suggest long term use of synthetics are equally beneficial to the soil. There is no mention of the nutritional differences in organically produced fruit/veggies vs synthetic either.

    The burden of proof rests on those making the claim, so I’ll stick to emulating the only life process to evolve on our planet over millions of years. Plus I have the anecdotal evidence in my garden.

    Thanks for the post though, made me do some thinking.


    • I am sorry but your comment “major differences in nutrient uptake process” is incorrect. Commercial fertilizers dissolve in water and become ions. the ions are then absorbed by plant roots. Organic material is broken down and releases the exact same ions, which are absorbed by plant roots in exactly the same way, because they are identical ions.

      The statement “Synthetic Nitrates and Ammonium Salts have to be in the proper PH range for a plant to most effectively absorb them. ” is not correct. It is not the ions that need to be at a particular pH range. It is true that if the pH is too extreme, ions get absorbed by soil and are less available to plant roots, but it is the pH of the soil solution ie the water around soil, that is important. If the pH of this soil solution is too high for a specific ion to be free, then this is exactly the same for both synthetic sources and organic sources. This comment applies mostly to the metal ions like iron and magnesium, not to nitrates or ammonium.

      Note: the last statement is not correct. Nitrogen availability is also pH dependent.

      Re: “There are plenty of scholarly studies that suggest organics are better for long term soil health. ” – absolutely correct. I never said organic is not better for the long term health of soil. Unfortunately most people do not understand why this is the case. You can read more about that here https://www.gardenmyths.com/organic-fertilizer-real-value/

      Re: “here is no mention of the nutritional differences in organically produced fruit/veggies vs synthetic either. ” – correct. That is because there is no nutritional difference.

  5. My understanding is the organic fertilizer remains in the soil, releasing nutrients as the molecules are broken down into the nutrients for uptake by the plants. The nutrients not absorbed can leach away with water. Manufactured fertilizers add the nutrients directly to the soil, and can be leached away by water.

    If that is true, then the use of organic material should have fewer nutrients leached from the soil by virtue of smaller quantities released at a time for the plants to absorb. If the plant absorbs the same amount of nutrient, it would be absorbing a higher percentage of those released by the organic material.

    Again, if true, eventually at least two things happen. Less inputs are needed in the long run under an organic program as you are adding to a continual supply rather than adding new nutrients from scratch, and less NPK is leached into the water systems. So the benefits of the organic method aren’t so much specifically for the plant as it is a potential cost-benefit and a water conservation benefit.

    Good conversation here

    • The leaching away of nutrients you describe is partially true. Nitrogen sources are very soluble and are easily leached away. Potassium moves much slower in soil and is only slowly leached away. Phosphate hardly moves at all. the rate of leaching depends on solubility and on how well they stick to soil, and humus particles.

      But in general organic fertilizer – provided it is in the form of large molecules will leach away slower. Your conclusion is correct – organic is better for the environment due to less leaching. Cost is a more complex issue.

  6. Lovely lily! Interesting how you spell it in american english! Perhaps I am out of step as I know you are in Canada!

    • One of the problems being Canadian is that we spell things like the Brits, but most things we read are written by Americans–and we get confused. I am trying to use American spelling.

      In the case of Lily–I just misspelled it. I a better gardener than a speller 🙂

  7. what about exudates? the plant gives them to microlife so they can be more abundant so that they can break down organic material for them. plus science is not everything.

    • I am not sure how exudates apply to the current topic? Plants do produce exudates from the roots and these chemicals do control the type of microbes that grow around the roots. One of the things plants produce are various kinds of sugar to feed the microbes. In addition to sugar, the microbes need a source of nitrogen. They can’t tell the difference between nitrogen from an organic source or nitrogen from a synthetic source–because both are exactly the same.

      Yes, the microbes break down organic compounds so that plants can use the nutrients–this is discussed in https://www.gardenmyths.com/what-is-the-real-value-of-organic-fertilizer/ .

      You say “science is not everything”. That is true, but when it comes to understanding plants I can’t think of anything other than science that can be used to verify and understand observations and facts.

    • Your question gave me a chuckle. If I were a plant, and I were intelligent, then I might know this for a fact!

      First of all plants are not intelligent. They do some things that are similar to what humans and animals do, but there is absolutely no evidence of intelligence.

      How do I know plants can’t tell the difference between an organic nitrogen molecule and an inorganic one? That is simple. None of the chemical testing that we do can tell one molecule from another–they are completely identical–I do have a chemistry background.

      That probably did not convince you so consider this. Lets say they are different. I add some commercial nitrogen fertilizer to my plant. It absorbs the nitrogen–this can’t be disputed since commercial nitrogen does grow plants. This plant then dies and is put on the compost heap. It decomposes and the compost produced is put back into the garden. As the plant decomposes further, the nitrogen molecule, which is now organic, is absorbed by another plant. Is this molecule organic or inorganic? It started as commercial fertilizer and the plant made it into an organic molecule, which then degraded by into a nitrogen molecule.

      Still not convinced? Go back and review your basic chemistry class. Elements are stable molecules that cannot be changed. A nitrogen molecule is a nitrogen molecules no matter where it comes from. Except for some atomic differences, which have no effect here, all nitrogen molecules are identical.

      You do not have to be a plant to know this–basic first year chemistry dictates this to be true.

      • I just want to say, “Thank you,” for your sensible explanation. I have had this conversation many times with differently minded people and it is refreshing to meet another person who understands elements, molecules and common sense.

      • There are many definitions of intelligence.
        One is the speed and depth to which an organism can solve a problem depending on input of information.
        A plant can meet its complex needs efficiently by controlling its overall outputs and intakes in a way that convinces me that it is an “intelligent” organism. I don’t think it is a difference in the understanding of plants, but rather in our understanding of intelligence. Thanks, I have an interest in gardening myths as a science teacher and this is the first day that I found your blog and find it interesting and well argued.

        • Intelligence also implies being able to evaluate the data and reacting to it differently. Plants always react the same way. They also can’t take all data into consideration. What plants do is simply react in a predetermined chemical way to stimuli.


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