Seabirds and some inland waterbirds nest in densely aggregated colonies. Nesting activities for a duration of months could lead to large quantities of guano deposition that affects the soil chemistry, flora and fauna. We assessed the effects of nesting Socotra Cormorants on soil invertebrates on Siniya Island, United Arab Emirates. Artificial substrate traps were set in nesting and non-nesting areas to sample invertebrates both before and after nesting had occurred. Diversity of soil invertebrate taxa decreased significantly in nesting areas compared to non-nesting areas after the commencement of nesting. This indicated that nesting activities had a negative effect on diversity. Among selected taxa, isopods and spiders decreased significantly in response to nesting activities. In contrast, ants were likely affected by habitat while beetles did not change significantly in response to nesting activities, suggesting that their numbers probably fluctuated in relation to seasonality. Ticks increased significantly but only in non-nesting areas. Thus, the impact of nesting varied between taxa depending on life history and seasonality. Our observations reflect the dynamic nature of invertebrate abundance that is affected by seasonality and the hyper-abundance of nesting seabirds.