Plants need nitrogen, phosphorus, and potassium, as well as micronutrients and symbiotic relationships with fungi and other organisms to flourish, but getting enough nitrogen, and particularly synchronization so that plants get enough nitrogen at the right time (when plants need it most), is likely the greatest challenge for organic farmers.Crop rotation(Crop rotation is the practice of growing a series of dissimilar types of crops in the same area in sequential seasons for various benefits such as to avoid the build up of pathogens and pests that often occurs when one species is continuously cropped.

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Crop rotation also seeks to balance the fertility demands of various crops to avoid excessive depletion of soil nutrients. A traditional component of crop rotation is the replenishment of nitrogen  through the use of green manure in sequence with cereals and other crops. It is one component of polyculture. Crop rotation can also improve soil structure and fertility by alternating deep-rooted and shallow-rooted plants.) and green manure ("cover crops") help to provide nitrogen through legumes (more precisely, the Fabaceae family) which fix nitrogen from the atmosphere through symbiosis with the bacteria rhizobia.

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Intercropping, which is sometimes used for insect and disease control, can also increase soil nutrients, but the competition between the legume and the crop can be problematic and wider spacing between crop rows is required. Crop residues can be ploughed back into the soil, and different plants leave different amounts of nitrogen, potentially aiding synchronization.

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Organic farmers also use animal manure, certain processed fertilizers such as seed meal and various mineral powders such as rock phosphate and greensand, a naturally occurring form of potash which provides potassium. Altogether these methods help to control erosion. In some cases pH may need to be amended. Natural pH amendments include lime and sulfur, but in the U.S. some synthetically compounds such as iron sulfate, aluminum sulfate, magnesium sulfate, and soluble boron products are allowed in organic farming.
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Mixed farms with both livestock and crops can operate as ley farms, whereby the land gathers fertility through growing nitrogen-fixing forage grasses such as white clover or alfalfa and grows cash crops or cereals when fertility is established.Farms without livestock ("stockless") may find it more difficult to maintain fertility, and may rely more on external inputs such as imported manure as well as grain legumes and green manures, although grain legumes may fix limited nitrogen because they are harvested.Horticultural farms growing fruits and vegetables which operate in protected conditions are often even more reliant upon external inputs.

Weed control

After nutrient supply, weed control is the second priority for farmers.Techniques for controlling weeds have varying levels of effectiveness and include handweeding, mulch, corn gluten meal, a natural preemergence herbicide, flame, garlic and clove oil, borax, pelargonic acid, solarization (which involves spreading clear plastic across the ground in hot weather for 4–6 weeks), vinegar, and various other homemade remedies. One recent innovation in rice farming is to introduce ducks and fish to wet paddy fields, which eat both weeds and insects.

KRISHI MITRA