Understanding the spatial distribution of soil protozoa under the snow cover is important for estimation of ecosystem responses to climate change and interpretation of results of field experiments. This work explores spatial patterns of soil testate amoebae under the snow cover at the plot scale (the range of metres) in arctic tundra (Qeqertarsuaq/Disko Island, West Greenland). To explain spatial patterns in abundance, species diversity and assemblage composition of testate amoebae, we measured microtopography, snow depth and substrate density. The results indicate that the abundance of active testate amoebae under the snow cover was quite low. The empty shell assemblage was characterised by the presence of linear spatial trends in the species composition across the site, whereas no patterns were detected within the plot. The distribution of the abundance and the species diversity were unstructured. The linear trends in the species composition corresponded to the site microtopography and were controlled by the topography-related soil moisture. Snow depth also affected the linear trends presumably by controlling soil temperatures. Overall, the results suggest that population processes do not generate spatial patterns in protozoan assemblages at the plot scale so that protozoan distribution can be considered random at macroscopically homogeneous plots.