Bees are often exposed to pesticides affecting physiological functions and molecular mechanisms. Studies showed a potential link between altered expression of energy metabolism related transcripts and increased homing flight time of foragers exposed to pesticides. In this study, we investigated the effects of thiamethoxam and pyraclostrobin on longevity, flight behavior, and expression of transcripts involved in endocrine regulation (hbg-3, buffy, vitellogenin) and energy metabolism (cox5a, cox5b, cox17) using radio frequency identification (RFID) technology and quantitative polymerase chain reaction. Parallel, a laboratory study was conducted investigating whether pesticide exposure alone without the influence of flight activity caused similar expression patterns as in the RFID experiment. No significant effect on survival, homing flight duration, or return rate of exposed bees was detected. The overall time foragers spent outside the hive was significantly reduced post-exposure. Irrespective of the treatment group, a correlation was observed between cox5a, cox5b, cox17 and hbg-3 expression and prolonged homing flight duration. Our results suggest that flight behavior can impact gene expression and exposure to pesticides adversely affects the expression of genes that are important for maintaining optimal flight capacity. Our laboratory-based experiment showed significantly altered expression levels of cox5a, cox6c, and cox17. However, further work is needed to identify transcriptional profiles responsible for prolonged homing flight duration.