Offspring sex-ratio is a key life-history trait that shows considerable variation among many bird species. Habitat quality is one of the numerous environmental factors acting on bias in sex-ratios in passerines. For the great tit Parrs major, southern French apple orchards constitute both feeding and breeding habitats of considerably varying quality depending on the annual amount of chemical pesticides used for pest control, which have both direct (toxicity) and indirect (lower prey availability) effects on bird populations. In a two-year study, we specifically assessed the effect of three pest management strategies involving high (conventional), moderate (IPM) and no (organic) chemical pesticide inputs on fledgling sex-ratio using molecular sexing techniques. We found that great tit populations had significant variations in fledgling sex-ratio across our range of habitat quality, with conventional apple orchards producing a more biased sex-ratio towards daughters than IPM and organic orchards. Estimates of maternal traits (female body condition, first egg-laying date, clutch size and hatching rate) were also analysed but they were not significant predictors of brood sex-ratio. This study supports the sensitivity of bird tertiary sex-ratio to habitat quality. It also suggests that highly pesticide-treated agro-ecosystems may be poorer habitats for temperate insectivorous bird species, We provide further evidence that reducing chemical pressure might mitigate anthropogenic impacts on bird life-histories and population dynamics.