Soil samples (varying in granularity) from four natural sites were cultured in microcosms to determine small-scale patchiness in abundance and diversity of gymnamoebae. Eighty grams of the same thoroughly mixed soil, either moistened with distilled water (− nutrients) or supplemented with an equivalent vol. of organically enriched water ( nutrients), were placed in covered glass jars and incubated for 14 d (25 °C). Abundances (number/gram soil) were assessed in each of 3 core samples (5–10 mm apart). Assay precision was estimated to be ± 4%. Abundances were similar in the 3 closely-spaced samples, but occasional samples had higher abundances, probably representing localized enriched sites (“nutrient hot spots”). Diversity within the triplicate, closely spaced samples varied substantially. Mean abundance and diversity of amoebae were consistently higher in organically enriched soil and in soil of increasing granularity. Field samples collected directly from two of the sites showed similar patterns of abundance and diversity as found in the experimental studies, indicating substantial small-scale compartmentalization of soil protist communities. These data provide evidence of soil eukaryotic microbiocoenoses and indicate that soil microfauna may encounter wide variations in resources and prey communities as they migrate within small distances of several millimeters or less.