Pesticide residues in fish muscle are an environmental and a health safety concern which requires analytical methods presenting high sensitivity and low limits of quantification. In this study, adapted QuEChERS method, coupled to liquid chromatography tandem mass spectrometry (Scheduled MRM-5500 QTRAP), was developed to quantify 13 pesticides (azoxystrobin, clomazone, diflufenican, dimethachlor, carbendazim, iprodion, isoproturon, mesosulfuron-methyl, metazachlor, napropamid, quizalofop and thifensulfuron-methyl) in muscle of fish. Quantification limits were below 1 ng g−1 except for clomazone (1.8 ng g−1) and quizalofop (7.4 ng g−1). Best recoveries were observed for perch (>80%) and roach (>68%), except for thifensulfuron-methyl. Lower recoveries had been observed for carp (6% to 86%). Relative standard deviation was lower than 28% for intra-day and 29% for inter-day analysis, respectively. This method was successfully tested on three fish species, naturally or orally exposed: roach (Rutilus rutilus), perch (Perca fluviatilis) and carp (Cyprinus carpio). Few levels were observed in fish naturally exposed, but carp and perch orally contaminated showed measurable levels in their muscles.