Abstract Soil fauna are a key component of soil biodiversity and a driver of soil functioning. While the importance of soil fauna is well recognized, quantitative estimates of the role of soil fauna on soil biogeochemical processes, such as plant litter decomposition, are limited by methodological constraints. The addition of naphthalene, a polycyclic aromatic hydrocarbon (C10H8), to suppress soil fauna has been used for decades in decomposition experiments, but its efficacy remains questioned. In fact, we lack a rigorous field assessment of the efficacy of naphthalene additions for soil fauna suppression and potential non-target effects on the soil microbial community and carbon cycling. We added naphthalene at a high rate (477gm−2) monthly for 23 months on the bare soil surface of a tallgrass prairie. We determined the effect of such additions on the abundance of nematodes and micro-arthropods along the soil profile to a depth of 20cm at 11, 16 and 23 months after initiating naphthalene application. We used the variation in the natural 13C abundance of the naphthalene (δ13C – 25.5‰) as compared to the native soil (δ13C∼−17‰) to quantify naphthalene contribution to soil CO2 efflux and microbial biomarkers (PLFA). Naphthalene addition significantly reduced the abundance of oribatid mites (−45%), predatory mites (−52%) and springtails (−49%), but did not affect nematode abundance. The 13C abundance of a few Gram-negative (cy17:0, 18:1ω7c, 16:1ω7c), Gram-positive (a15:0, i15:0) and Actinobacteria (10Me-16:0, 10Me-18:0) PLFA markers decreased significantly in naphthalene treated plots, indicating bacterial utilization of naphthalene-derived C. Mixing models showed this contribution to be highly variable, with the highest naphthalene-C incorporation for Gram negative bacteria. Naphthalene-C was not incorporated in fungal PLFAs. This microbial utilization did not affect overall microbial abundance, community structure or activity, estimated as soil respiration. This experiment proves that naphthalene addition is a feasible method to reduce soil micro-arthropods in the field, with negligible direct effects on soil nematodes, microbial abundance and C dynamics.