Bees are essential for agricultural productivity and ecosystem stability, but pesticides contribute significantly to recent bee declines worldwide. Despite the importance of balancing the beneficial and detrimental impacts of pesticides, we have limited understanding of the mechanisms through which pesticides affect pollinators, how exposure to multiple environmental stressors may worsen their effects, or how effects differ between species. Detailed insight is beyond the reach of traditional pesticide susceptibility evaluation approaches, because they only measure few organism- or colony-level effects. Instead, we will use whole-transcriptome gene expression profiling (RNA-seq) in brain, midgut, and flight muscle, providing thousands of measurements per sample. We will first expose Bombus terrestris bumblebees to three individual pesticides (acetamiprid, sulfoxaflor, and flupyradifurone) and combinations of these compounds, simulating what occurs when neighbouring fields have different treatments. Second, we will test whether pesticide effects are exacerbated when simulating a warmer climate or if low quality food is available - as is common around monocultures. Finally, we will perform similar experiments in the solitary red mason bee Osmia bicornis. We hypothesise that we will detect previously unknown effects of the pesticides, and non-linear interactions that lead to substantial differences in qualities and intensities of effects between pesticides, combination treatments, and species. Our work will provide detailed insight into the diverse mechanisms by which the pesticides affect bees, how interactions with other environmental stressors may worsen pesticide effects, and how effects and interactions may differ between species. This research will provide clarity about whether such factors must be considered during pesticide evaluation. Furthermore, our approach pioneers a powerful new toolkit for pesticide research and assessment.