A soil amendment refers to any material added to the soil to improve its physical or chemical properties.

With fresh fruits and vegetables, food safety concerns are most often associated with biological contamination by pathogens in manure-based soil amendments. However, chemical hazards associated with inorganic fertilizers can represent a chemical risk to crops as well as to those workers who apply the fertilizers. Many inorganic fertilizers are federally regulated so the first rule is to always follow the label because the label is the law (1). Proper storage practices and controlling access to these chemicals is also important to meet federal requirements and reduce the chance of chemical contamination on the farm.

Manure-based soil amendments can harbor pathogens that can cause illness in humans and may contaminate produce when introduced into the production environment. This overview is intended to provide general guidelines and recommendations to reduce the likelihood of produce microbial contamination when using manure-based soil amendments.

  • If it is unknown whether the manure-based soil amendment is raw or fully composted, handle it as if it were raw manure.
  • Recommended time intervals from application of raw manure to the harvest of the produce crop vary from 90 days to five years. The recommended application intervals are discussed in more detail below.
  • Composting manure using a controlled, validated method can significantly reduce the risk of contamination.
  • Recordkeeping is important for all soil amendment applications. Document what, where, when, how, and how much was applied. For compost, the composting process including times, temperatures, and turnings must be documented.

Raw Manure  

When a crop is grown on land on which raw manure has recently been applied, there is a risk that the crop could be contaminated because of the likelihood of pathogens being present. If raw manure is used as a soil amendment or fertilizer, it should never be applied during the growing season and it should always be incorporated into the soil within 72 hours after application. The interval between raw manure application and harvest should be maximized. The required time frame between application and harvest varies throughout the industry. The Leafy Greens Marketing Agreement (LGMA) requires an application interval of at least one year (2). The National Organic Program (NOP) recommends applications be at least 90 days before harvest for crops that have edible portions which do not come in contact with the soil and at least 120 days before harvest of crops that have edible portions which do come in contact with the soil (crops in or near the soil are most vulnerable to contamination) (3). The Food Safety Modernization Act (FSMA) Produce Safety Rule (PSR) requires that raw manure be applied in a manner that does not contact produce (4). The Rule does not indicate an application interval for raw manure that will not contact produce; however, the NOP recommendations (above) can be followed. Some research shows that pathogens can persist in the soil well beyond the NOP application interval (5-8), therefore some leafy green buyers require up to a five year application interval (9).

Aside from raw manure purposely applied to fields, it is important to consider manure that may enter the field through runoff, wildlife or domesticated animal intrusion, or movement from adjacent lands that have domesticated animals. Please see the Wildlife and Animal Management Decision Tree and the Land Use Decision Tree to assess these risks.


Composting animal manure can reduce microbial pathogens and greatly reduce the risk of contamination to fruit and vegetable crops. Simply piling or aging manure without actively managing and monitoring it is not composting and therefore aged manure must be handled the same way as raw manure. If the same equipment or tools are used on raw manure as on cured or curing piles, be sure to clean and sanitize them after use on raw manure to avoid contamination of composted manure piles.

Compost must maintain a minimum temperature of 131 °F for 3 consecutive days (enclosed system) or 15 days (windrow system), during which period the composting materials must be turned a minimum of five times (10). After these steps, the compost pile should cure for 45 days. Finished and curing compost piles should be covered in order to prevent recontamination. Acceptable organic materials for compost include, but are not limited to: animal manure, by-products of agricultural commodities processing, yard debris, and kitchen wastes. Detailed records of on-farm treated compost must be kept to document that process controls (temperature and moisture management, dates turned, and the duration of high temperatures) were achieved (11). The Northeast Recycling Council (12), and the Cornell Waste Management Institute’s Compost Fact Sheet Series 1–8 (13) provide specific guidelines and tips for composting manure to assure its safe and effective use as a fertilizer.

Leachates and Teas

Leachates and teas are used as foliar fertilizers and soil amendments to suppress pests and diseases, as well as to enhance soil biology. Compost leachate is the liquid coming out of compost when water from irrigation, rain, or snow filters through the compost. Compost tea is made from compost steeped in water. There are two basic types of compost tea, aerated and non-aerated.

  • Aerated tea = manure/compost mixed with water (1:10-50) and then aerated by injection or re-circulated water for 12 to 24 hours (14)
  • Non-aerated tea = manure/compost mixed with water (1:3-10) and left untouched for several days (1 to 3 weeks) (14)

To reduce the risk of pathogen contamination of produce:

  1. Use potable water, or the microbial equivalent of potable water, when mixing compost teas. In order for the tea to be considered a treated soil amendment, the FSMA PSR requires that the water used to make the tea has no detectable generic E.coli in 100 mL, determined through testing (15).
  2. Use properly composted manure. There is no application interval restriction on using compost tea made from properly composted manure and potable water, though it should only contact the soil and not the edible portion of the crop.
  3. For leafy greens, follow the Leafy Greens Marketing Agreement guidance which states that raw manure teas shall NOT be directly applied to the edible portions of lettuce and leafy greens and must follow the one-year application interval (2).
  4. If additives are used (molasses, yeast, etc.), follow the same application intervals as raw manure (3, 15).
  5. Compost leachate may be applied to the soil using the NOP 90/120 day rule. It must NOT be applied directly to plants (3).
  6. Teas must NOT be applied to edible seed sprouts.


Recordkeeping should always be part of your food safety program. Developing a recordkeeping system that is easy to use will encourage soil amendment applicators to properly document their activities and support the implementation of a farm food safety plan.

Documentation should include:

  • Type of soil amendment being applied
  • Fields receiving application
  • Date of application
  • Rate (quantity applied per acre)
  • Method of application
  • What crops will be planted

Documentation must include (11, 20):

  • For on-farm treatment of soil amendments, growers must keep measurements of key composting parameters such as time, temperature, and turnings.
  • For treated soil amendments that are received from a third party, growers must obtain and keep documentation (such as a Certificate of Conformance) at least annually that the soil amendment was treated using a scientifically valid process carried out with appropriate process monitoring AND that the soil amendment was handled, conveyed, and stored in a manner and location to minimize the risk of contamination with an untreated or in-process soil amendment.

The information in the template food safety plan, SOPs, and recordkeeping logs are examples you can use. They are not intended to be used directly. Tailor each to fit your farm operation and practices. These documents are guidance for risk reduction and for educational use only. These documents are not regulatory and are not intended to be used as audit metrics. These documents are subject to change without notice based on the best available science.

  1. Environmental Protection Agency. Summary of the Federal Insecticide, Fungicide, and Rodenticide Act. 7 U.S.C. § 136.
  2. Leafy Greens Marketing Agreement. Commodity Specific Food Safety Guidelines for the Production and Harvest of Lettuce and Leafy Greens. 2020.
  3. National Organic Program. CFR § 205.203. 2012. Soil Fertility and Crop Nutrient Management Practice Standard.
  4. FSMA, Produce Safety Rule. 21 CFR § 112.56. 2015.
  5. Fukushima HK, Hoshina K, Gomyoda M. Long-Term Survival of Shiga Toxin-Producing Escherichia coli O26, O111, and O157 in Bovine Feces. Appl Environ Microbiol. 1999. 65(11):5177–81.
  6. Gagliardi JV, Karns JS. Leaching of Escherichia coli O157:H7 in Diverse Soils under Various Agricultural Management Practices. Appl Environ Microbiol. 2010. 66(3):877–83.
  7. Islam M, Doyle MP, Phatak SC, Millner P, Jiang X. Survival of Escherichia coli O157:H7 in Soil and on Carrots and Onions Grown in Fields Treated with Contaminated Manure Composts or Irrigation Water. Food Microbiol. 2005. 22:63–70.
  8. Wang G, Zhao T, Doyle MP. Fate of enterohemorrhagic Escherichia coli O157:H7 in bovine feces. Appl Environ Microbiol. 1996 Jul. 62(7):2567–70.
  9. Bihn EA. Survey of Current Water Use Practices on Fresh Fruit and Vegetable Farms and Evaluation of Microbiological Quality of Surface Waters Intended for Fresh Produce Production. Thesis [Ph.D.], Cornell University. 2011.
  10. FSMA, Produce Safety Rule. 21 CFR § 112.54. 2015.
  11. FSMA, Produce Safety Rule. 21 CFR § 112.60. 2015.
  12. Manure Management for Small Hobby Farms. Northeast Recycling Council. 2019. 
  13. Cornell Waste Management Institute factsheets
  14. Formal Recommendation by the National Organic Standards Board (NOSB) to the National Organic Program (NOP). 
  15. FSMA, Produce Safety Rule. 21 CFR § 112.51. 2015.
  16. NRCS. Waste Utilization. Code 633. 2002.
  17. NRCS. Nutrient Management. Code 590. 2012.
  18. FSMA, Produce Safety Rule. 21 CFR § 112.52. 2015.
  19. FSMA, Produce Safety Rule. 21 CFR § 112.55. 2015.
  20. Clements D, Acuña-Maldonado L, Fisk C, Stoeckel D, Wall G, Woods K, and Bihn E. FSMA Produce Safety Rule: Documentation Requirements for Commercial Soil Amendment Suppliers. Produce Safety Alliance; 2019.