Due to the expansion of sugarcane crops and the high costs of agricultural inputs, an alternative for fertilization of the soil is the use of humic substances (HS) because they improve its physical-chemical properties. The objective of this study was to assess the biological degradation of fipronil in soil supplemented with HS. For determination of fipronil and its metabolites, we validated a quick, easy, cheap, effective, rugged, and safe gas chromatography-mass spectrometry (QuEChERS/GC-MS) method, which yielded detection and quantification limits of 15.0 and 62.5 ng g −1 , respectively. The method presented linearity of 0.99, precision between 1.5 and 10.9%, while the recovery ranged from 78 to 98%, with precision (relative standard deviation (RSD)) < 5%. The strain B. thailandensis of Burkholderia sp. grew under typical conditions for degradation of fipronil. Eight treatments assessed the degradation by B. thailandensis in the presence of HS. The metabolites produced in the experiment, although detected, could not be quantified because they were below the limit of quantification of the method. Our results showed that B. thailandensis has the potential to degrade fipronil, and that HS is not toxic to the microbiota, and does not inactivate fipronil.