One of the greatest benefits of complete and balanced crop fertilization, aside from increasing crop yields and improving farmer profit potential, is its effect on soil organic matter.

Both organic and inorganic (mineral) fertilizer sources contribute to the buildup of organic matter in soils. There is widespread public misconception that organic agriculture is more environmentally friendly and maintains improved levels of soil organic matter. However, there is no generally accepted scientific evidence to support the superiority of either organic or inorganic plant nutrient sources. In fact, long-term experiments gathered from around the world indicate that sustained yields and soil productivity can be accomplished with balanced nutrient applications; using either animal manure and/or commercially produced mineral fertilizers.

Organic fertilizers typically involves plant residues or livestock manure. The amount of nutrients that they deliver per kilo to the soil can never be accurately measured. Organic farming is less efficient and produces lower crop yields than farming with mineral fertilizers. This is partly because mineral fertilizers deliver far more essential nutrients per unit than does organic matter.

In addition, it is difficult to guarantee an optimal balance among or quality among nutrients using only organic sources. For example, providing enough nitrogen for a crop by applying manure would mean adding 4 to 5 times more potassium and phosphorous than is needed. Runoff can pollute waterways and the life they support.

Conversely, mineral fertilizers are chemically processed to meet crop requirements and can supply plant nutrients in exact, scientifically formulated quantities. Mineral fertilizers are generally cost effective, but require an upfront investment that may be difficult for small farmers without credit. Ideally, mineral fertilizers should be used together with organic fertilizers which improve soil structure and the soils water holding capacity. The precision that manufactured mineral fertilizers offer helps overcome the limitation of organic fertilizer.

Poor management of plant nutrients, whether organic or as mineral fertilizers, can mean loss of some nutrients to the environment. This can upset the balance of the natural ecosystems. But if a farmer uses appropriate agricultural practices, the crop will absorb most properly applied fertilizers.