Small lentic water bodies are important emitters of methane (CH₄), but the processes regulating CH₄ dynamics and their susceptibility to human-induced stressors are not fully understood. Bioturbation by chironomid larvae has been proposed as a potentially important factor controlling CH₄ dynamics in aquatic sediments. Chironomid abundance can be affected by the application of biocides for mosquito control, such as Bti (Bacillus thuringiensis var. israelensis). Previous research has attributed increases in CH₄ emissions after Bti application to reduced bioturbation by chironomids. In this study, we tested the effect of chironomid bioturbation and Bti addition on CH₄ production and emission from natural sediments. In a set of 15 microcosms, we compared CH₄ emission and production rates with high and low densities of chironomid larvae at the bioturbating stage, and standard and 5 x standard Bti dose, with sediments that contained neither larvae nor Bti. Regardless of larvae density, the chironomids did not affect CH₄ emission and production of the sediment, although both rates were more variable in the treatments with organisms. 5xBti dosage, however, led to a more than three-fold increase in CH₄ and CO₂ production rates, likely stimulated by bioavailable dissolved carbon in the Bti excipient. Our results suggest weak effects of bioturbating chironomid larvae on the CH₄ dynamics in aquatic ecosystems. Furthermore, our results point out towards potential functional implications of Bti for carbon cycling beyond those mediated by changes in the macroinvertebrate community.