Although pesticides are a key driver of bee decline globally, the contribution of non-insecticidal pesticides, specifically herbicides and fungicides, is poorly understood. The herbicide glyphosate and the fungicide prothioconazole are amongst the most widely used pesticides in Ireland. Consequently, characterising their impact on Ireland’s wild bee species is of urgent importance. Here, I investigated and characterised the impact of glyphosate and prothioconazole on the bumblebee B. terrestris at the molecular and organism level, in addition to two representative commercial formulations: Roundup Optima+® and Proline®, containing glyphosate and prothioconazole, respectively. Utilising mass spectrometry-based proteomics, DNA amplicon sequencing, and survival assays, I uncovered the impact of these pesticides and formulations on the digestive tract, brain, and fat body proteome, digestive tract microbiota, survival, behaviour, and food consumption in B. terrestris. Neither pesticide altered survival or food consumption, but prothioconazole altered behaviour at field-realistic concentrations. Further, all treatments led to microbiota dysbiosis. Glyphosate and Roundup Optima+® consistently altered oxidative stress regulation and mitochondrial proteins in all organs and led to decreases in structural proteins in the digestive tract. Both glyphosate-based treatments altered synaptic transmission and signaling in the brain, and protein biosynthesis and energy homeostasis in the fat body. However, differential impacts were also observed. Further, prothioconazole and Proline® had differential impacts on all key organs, indicating the impact of co-formulants in formulations and solvents used for pesticide solubility on bees, leading to significant alterations to detoxification, neurotransmitter biosynthesis and cytoskeletal proteins, and oxidative stress in the digestive tract, brain, and fat body, respectively. Overall, this research uncovered the impacts of glyphosate and prothioconazole, as well as representative formulations, on B. terrestris, and raised important questions on the complexities of pesticide impacts on bees when used as part of a formulation.