Living organisms play an essential role in soil formation. The numerous plants and animals living in the soil release minerals from the parent material from which soil is formed, supply organic matter, aid in the translocation (movement) and aeration of the soil, and help protect the soil from erosion. The types of organisms growing or living in the soil greatly influence the soil's physical and chemical characteristics. In fact, for mature soils in many parts of the world, the predominant type of natural vegetation is considered the most important direct influence on soil characteristics. For this reason, a soil scientist can tell a great deal about the attributes of the soil in any given area simply form knowing what kind of flora the soil supports. Thus prairies and tundra regions, which have characteristic vegetations, also have characteristic soils.

The quantity and total weight of soil flora generally exceed that of soil fauna. By far the most numerous and smallest of the plants living in soil are bacteria. Under favorable conditions, a million or more of these tiny, single-celled plants can inhabit each cubic centimeter of soil. It is the bacteria, more than any other organisms, that enable rock or other parent material to undergo the gradual transformation to soil. Some bacteria produce organic acids that directly attack parent material, breaking it down and releasing plant nutrients. Others decompose organic litter (debris) to form humus (nutrient-rich organic matter). A third group of bacteria inhabits the root systems of plants called legumes. These include many important agricultural crops, such as alfalfa, clover, soybeans, peas, and peanuts. The bacteria that legumes host within their root nodules (small swellings on the root) change nitrogen gas from the atmosphere into nitrogen compounds that plants are able to metabolize, a process, known as nitrogen fixation, that makes the soil more fertile. Other microscopic plants also are important in soil development. For example, in highly acidic soils where few bacteria can survive, fungi frequently become the chief decomposers of organic matter.

More complex forms of vegetation play several vital roles with respect to the soil. Tress, grass, and other large plants supply the bulk of the soil's humus. The minerals released as these plants decompose on the surface constitute an important nutrient source for succeeding generations of plants as well as for other soil organisms. In addition, trees can extend their roots deep within the soil and bring up nutrients from far below the surface. These nutrients eventually enrich the surface soil when the tree drops its leaves or when it dies and decomposes. Finally, trees perform the vital function of slowing water runoff and holding the soil in place with their root systems, thus combating erosion. The increased erosion that often accompanies agricultural use of sloping land is principally caused by the removal of its protective cover of natural vegetation.

Animals also influence soil composition. The faunal counterparts of bacteria are protozoa. These single-celled organisms are the most numerous representatives of the animal kingdom, and, like bacteria, a million or more can sometimes inhabit each cubic centimeter of soil. Protozoa feed on organic matter and hasten its decomposition. Among other soil-dwelling animals, the earthworm is probably the most important. Under exceptionally favorable conditions, up to a million earthworms (with a total body weight exceeding 450 kilograms) may inhabit an acre of soil. Earthworms ingest large quantities of soil, chemically alter it, and excrete it as organic matter called casts. The casts form a high-quality natural fertilizer. In addition, earthworms mix of soil both vertically and horizontally, improving aeration and drainage.

Insects such as ants and termites also can be exceedingly numerous under favorable climatic and soil conditions. In addition, mammals such as moles, field mice, gophers, and prairie dogs sometimes are present in sufficient numbers to have significant impact on the soil. These animals primarily work the soil mechanically. As a result, the soil is aerated broken up, fertilized, and brought to the surface, hastening soil development.

活的有机体在土壤形成的过程中起到关键的作用。大量的生活在土壤里的植物和动物从土壤形成的母质层释放矿物质，提供有机物，帮助土壤的运动和通风，并且帮助保护土壤免受侵蚀。在土壤里生长或生活的有机体的种类极大地影响了土壤的物理和化学特性。实际上，对于各地的成熟土壤而言，占据优势地位的植被物种被认为是影响土壤特性的最重要的直接因素。因为这个原因，土壤学家仅仅通过土壤所支持的植物群种类就能推断出关于任意给定地区土壤属性的大量信息。因此，拥有特征性植被的大草原和苔原地区也同样拥有特征性土壤。

一片土壤的植物群的数量和总重量一般会超过其承载的动物群的对应数值。至今为止，数量最多和体积最小的土壤生物是细菌。在适宜的条件下，一立方厘米体积的土壤可以容纳一百万或者更多的这种小小的单细胞生物。是这种细菌，而不是其他的有机体，使得岩石或者母质逐渐转化为土壤。一些细菌会分泌有机酸，这些有机酸直接腐蚀母质层，把它们分解掉并释放营养物质。其他的细菌则可以分解有机垃圾（残骸）来形成腐殖质（富含营养的有机物质）。第三种细菌存在于植物的根系里，被称作豆科植物。这些植物包括很多重要的农作物，比如说苜蓿，三叶草，大豆，豌豆和花生。寄生在豆科植物根瘤（根茎上的小肿块）中的细菌把空气中的氮气转化成植物可用以新陈代谢的含氮化合物。这个过程被称为固氮作用，可以使得土壤更肥沃。其他的微生物在土壤发育过程中也十分重要。例如，在酸度很高的土壤中，几乎没有细菌可以存活，真菌经常就变成了有机物的主要分解者。

还有更复杂的植被也在土壤形成方面起到了至关重要的作用。树木枝条，草地，还有其他的大型植物为土壤提供了大量的腐殖质。这些植物在表面分解时产生的矿物质为后代的植物以及其他土壤内的有机体提供了营养。另外，树木可以把根延伸到土壤里，并且把土壤深处的营养物质带到土壤表面。这些营养经过树木落叶或者死亡分解的过程，最后会留在表层土里面。最后一点，树木在减缓水流速度和保持土壤方面有关键的作用，这就可以抵抗土壤的流失。日益严重的水土流失经常和斜坡上的农业用地一起出现，这往往是由自然植被保护层的砍伐而导致的。

动物也会影响土壤组成。与细菌在微生物界的地位相类似的是原生动物在动物界的地位。这些单细胞的有机体在自然界数量巨大。就像细菌一样，一立方厘米里可以生存百万个或更多的的原生动物。原生动物以有机物为食，并且同时加速其分解。在其他生活在土壤里的动物里，蚯蚓可能是最重要的。在一些异常的有利条件下，多达一百万条蚯蚓（总重量可以超过450千克）可以存活在一英亩土壤里。蚯蚓可以吃下大量的土壤，改变其化学成分，并且产生一种被称为casts的有机物质。这种casts形成了一种高质量的自然肥料。另外，蚯蚓会垂直地水平地搅拌土壤，这改善了土壤的通风和排水情况。

像蚂蚁和白蚁的昆虫在适宜的气候和土壤条件下数量也是很多的。另外，哺乳动物比如说鼹鼠，田鼠，囊地鼠以及北美草原土拨鼠有时候也会数量充足，对于土壤造成重要的影响。这些动物不自觉地在耕作着土壤。结果就是，土壤被打碎以便于通风，变得更加肥沃并且养料被带到表层土，这一切都加速了土壤的发育。