by Sara Runkel, CFSA Local Produce Safety Coordinator | Monday, Dec. 12, 2022 – 

Compost sits on top of a long bed

Winter is here, and while you may still be producing crops, hopefully, the pace of work on the farm has slowed a bit. As you reflect on how your 2022 season went and make plans for the 2023 growing season, now would be a good time to develop or review the fertility management plan for your farm. Providing the correct amounts of all the nutrients crops need when they need them most takes planning. Animal-based fertilizers are usually a key component of a sustainable farm’s fertility management plan. They can provide critical plant nutrients; depending on the source, they can also help build organic matter in the soil.

There are many different options when it comes to sourcing these fertilizers. You may already be factoring in cost and availability when choosing your fertilizers, but have you thought about food safety?

If you grow produce, which includes fruits, vegetables, herbs, and mushrooms, food safety is something you should keep in mind when using animal-based fertilizers because of their potential to contaminate produce with microorganisms that can make people sick. These include pathogenic E. coli, Salmonella, Campylobacter, and Listeria, all bacteria associated with animal manure.

When assessing the food safety risks of your fertility management plan, you should think about four broad questions.


1. What Animal-Based Fertilizers Are You Using?

Many animal-based fertilizers are available for you to use on the farm. Some are manure-based, including raw and aged manure, compost that contains manure, and commercially processed fertilizers like bat guano. There are also several animal by-product-based fertilizers, including blood meal, fish emulsion, bone meal, and feather meal. The food safety risks of these fertilizers can be divided into two categories, treated and untreated. Treated animal-based fertilizers have gone through a process to kill pathogens that might make us sick. Heat is the most common form of treatment.

Manure can be a great fertilizer source, especially if you raise livestock or have a neighbor willing to share. The fertility management considerations for manure were discussed in last month’s article, The Quick & Dirty on Improving Nitrogen Management. When considering food safety, raw and aged manure are considered untreated and have higher food safety risks. Not all manures are contaminated with human pathogens, but there is a chance, and it is not feasible to test all of the manure you use for the full list of human pathogens. Instead, it is better to assume that manures are likely to be contaminated and minimize food safety risks associated with their use.

Not All Aged Manure Is Compost

What about aged manure, isn’t that compost? No, composting is a controlled process that breaks down organic materials to create a stabilized soil amendment with chemical, physical, and biological benefits. One common way of producing compost involves bringing the materials up to a designated temperature (e.g., 131° F) for a specific period (3-15 days, depending on how many times the pile is turned), followed by a curing period. Composting has many benefits. It reduces biomass, stabilizes organic matter, and can reduce viable weeds, seeds, and human and plant pathogens if done properly. Simply piling manure up and letting it age passively does not yield the same benefits as composting. In fact, research has found that stored manure can have higher levels of pathogens than fresh manure.

If you are producing animal-based compost on your farm, it is important to consider whether or not you will be able to bring all of the compost materials to the correct temperature and for a long enough time to kill pathogens. If you can’t, you can still use the compost, but you should consider it an untreated fertilizer.

Foliar Sprays

When using compost tea or other animal-based fertilizers that are applied as foliar spray, you need to consider the quality of the water you use to prepare the solution, the treatment status of the compost/fertilizer, and the addition of materials like molasses or yeast. This is especially true if you are applying these materials to the edible portion of the crop. For example, if you are foliar feeding leafy greens, you want to use treated compost or fertilizer material and water with no detectable generic E. coli. The same type of water that you use for handwashing or washing produce. You should also refrain from including additives like molasses and yeast for this type of application. They are added to feed the microbes in the tea, which is great for beneficial microbes but also increases the risk of growing the microbes that can make us sick.

“Stored manure can have higher levels of pathogens than fresh manure.”

When purchasing animal-based fertilizer, including compost, it is a good idea to check with your supplier or the manufacturer to see if it was treated to kill human pathogens. Knowing the treatment status of your fertilizer will help you decide how to best use it in a way that minimizes food safety risks.

Now that you have decided on what fertilizers you will use and know if they are treated or untreated, you can think about what the next question might be.


2. What Crops Are We Applying These Fertilizers To, & When?

Produce that is usually eaten raw, like berries, salad greens, melons, carrots, radishes, and so many more, are more likely to make consumers sick if they are contaminated with human pathogens. This is because there is no kill step in the preparation process. When using animal-based fertilizers on these crops, especially untreated fertilizers, it is important to take into consideration the timing of application. One option for minimizing risk with these fertilizers is to apply them to other crops in your rotation. For example, you could apply them in the fall to growing cover crops, use them to fertilize row crops, or a crop like potatoes which is not usually eaten raw.

A red tractor applying manure to a plowed field using a manure spreader attachment.

If you are going to use them for fresh produce production, the more time you can leave between the application of untreated fertilizers and harvest, the better. At a minimum, you can use the National Organic Program rule as a guide. Apply untreated fertilizers at least:

  • 120 days before harvest when the edible portion of the crop comes into contact with the ground (and fertilizer).
  • 90 days before harvest when the edible portion of the crop does not come into contact with the ground.


3. How Are They Being Applied?

In addition to the timing of application, the way in which you apply these fertilizers is also an opportunity to manage risk. Whether you are broadcasting, side-dressing, fertigating, or using a foliar spray, think about how the application method could pose a risk to the crop you are growing, adjacent crops, and water sources. Wind and water can both carry fertilizer and any pathogens that might be in it to adjacent growing areas, ponds, and rivers that are used for irrigation and even into areas where you are washing and packing produce.

Minimize Risks

Some ways you can minimize application risks are to incorporate fertilizers into the soil quickly after you broadcast, avoid applying when the ground is frozen or before a heavy rain event, only apply what you need, and don’t side-dress crops with untreated fertilizers when the edible portion of the crop comes into contact with the ground.

Keep Records

It is also a good idea to keep application records with information about when and where you applied fertilizer, what type of fertilizer you used, and at what rate. These records are an important part of a fertility management plan and are required for organic certification and third-party food safety audits. They help manage food safety risks on the farm by creating a paper trail that shows how you are using fertilizers in a way that minimizes contamination.


4. How Are These Fertilizers Handled and Stored?

It might seem like common sense to keep manure off food, even if you never directly apply untreated animal-based fertilizers to your produce crops. There are many opportunities for indirect contamination through cross-contamination of equipment, footwear, clothing, water sources, and produce production areas. Cross-contamination can be a food safety risk when contaminated items come into contact with produce or food contact surfaces. It can also be an issue if you handle and store both untreated and treated fertilizers. If treated fertilizers are unintentionally contaminated with untreated materials, food safety risks increase. You may end up applying the contaminated treated fertilizer in a way that can contaminate produce with pathogens.

Ways to Limit Cross-Contamination

You can limit cross-contamination by having separate shoes, gloves, tools, and equipment for handling fertilizer, especially raw/untreated animal-based materials (e.g., manure and incomplete compost). Tools can be color-coded, so it is easy to tell which ones are only for use with fertilizer. Store dedicated fertilizer tools away from harvest tools and produce washing and packing areas.

A large wooden bin inside a barn holds neatly organized hand tools.

If it is impossible to have a separate set of tools or equipment like a front-end loader or pickup truck, make sure you clean and sanitize these items before using them to handle produce.

Ensure workers wash their hands properly after handling animal-based fertilizers, especially raw/ untreated materials or contaminated equipment. They should also change clothing and shoes between activities and use separate gloves for handling compost and fertilizers.

Think about where you locate manure and compost piles.

  • Are they adjacent to produce production areas or uphill from them?
  • Are they close to a water source that you use for irrigation?
  • What about equipment and foot traffic around storage areas?
  • Do your compost piles attract animals like rodents or birds that might contaminate them?

Addressing each of these questions will help you minimize cross-contamination.



There are many benefits to using animal-based fertilizers in your fertility management plan. They are usually approved for use in organic systems, utilize waste products, and are a source of nutrients and organic matter (depending on the type used). Don’t let the potential food safety risks associated with them discourage you from using them. Know what the potential risks are and use them carefully so they don’t become a source of contamination on your farm.

If you think through how to address each of the four questions discussed above, you will be well on your way to minimizing food safety risks when using animal-based fertilizers.

If you have any questions about farm food safety, CFSA has many great resources available through our Food Safety Resource Hub. Our team is also available to help you improve food safety practices on your farm.