Ionic liquids are considered as a potential green replacement for traditional volatile organic solvents, but their impact on the environment is not sufficiently studied. The effect of the addition of aqueous solutions of different amounts (from 0% to 75%) of three ionic liquids, two based imidazolium, dimethylimidazolium dimethylphosphate ([MMIM][DMP] and 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) and choline dihydrogen phosphate ([Chol][DHP]) on the microbial activity of an acidic, organic soil, was determined in this work. For this propose, an isothermal microcalorimeter, TAM III of TA Instruments was used. This apparatus allows estimating the variation of the metabolic activity through the variation of the heat released after the addition of the ionic liquids (ILs) to the soil. The results showed that the most toxic IL is [BMIM][BF4] which presented a large stress effect and subsequent death on soil microorganisms for the highest concentration of the IL. On the contrary, [Chol][DHP] showed stimulation of the microbial activity for all the concentrations.