A decrease in biodiversity and density of terrestrial organisms with increasing altitude and latitude is a well-known ecogeographical pattern. However, studies of these trends are often taxonomically-biased toward well-known organisms and especially those with relatively large bodies, and environmental variability at the local scale may perturb these general effects. Here, we focus on understudied organisms—soil invertebrates—in Antarctic deserts, which are among the driest and coldest places on Earth. We sampled two remote Antarctic sites in the Darwin Glacier area and established an altitudinal gradient running from 210 to 836 m a.s.l. We measured soil geochemistry and organic matter content and linked these parameters with the presence of soil invertebrates. We found three general outcomes, two of which are consistent with general assumptions: (a) the hostile climatic condition of the Darwin Glacier region supports an extremely low diversity of soil metazoans represented by a single nematode species—Scottnema lindsayae; (b) soil geochemistry is the main factor influencing distribution of nematodes at the local scale. Contrary to our expectations, a positive correlation was found between nematode density and altitude. This last observation could be explained by an additional effect of soil moisture as we found this increased with altitude and may be caused by orographic clouds, which are present in this region. To the best of our knowledge such effects have been described in tropical and temperate regions. Potential effect of orographic clouds on soil properties in polar deserts may be a fruitful area of ecological research on soil fauna.