Apiculture and pollination services are seriously threatened by bee weakening and losses phenomena. In this context, a survey was performed on samples from beehives across French areas during the 2012-2016 growing seasons, primarily taken from symptomatic colonies. A total of 488 honeybees, beebread, and wax were analyzed for the presence of pesticide residues. A total of 13 analytes including neonicotinoids and pyrethroids insecticides together with some of their metabolites and the fungicide boscalid were screened within samples. Methodologies based on efficient modified quick, easy, cheap, effective, rugged, and safe extractions followed by an LC-MS/MS quantification were implemented for each matrix. Thirty-eight percent of the 125 bee samples, 61% of the 87 wax samples, and 77% of the 276 beebread samples contained at least one of the targeted pesticides. Beebread was the most contaminated matrix with an average of two pesticide detections by positive sample and a maximum of seven compounds for a sample. Neonicotinoids and boscalid were the most often detected pesticides, whatever the matrix. The comparison of neonicotinoid detections in samples collected before and after the partial neonicotinoid ban in France displays a decrease in the frequency of detections for contamination levels lower than 1 ng/g in beebread. For higher levels and other matrices, no tendency can be drawn.