The global decline of bumble bee species is attributed to a wide array of stressors, including pesticides and parasites. Determining the relative importance of particular stressors on bumble bee population health and pollination services is difficult in a field setting, as confounding factors limit causal attribution. Large-scale greenhouses provide an ideal alternative for conducting insect pollinator experiments, allowing for semi-field realism with fewer unmonitored variables. As bumble bees are commonly deployed for pollination in tomato greenhouses, this system presents an excellent environment to investigate the connections between agricultural pesticide use, bee health, and pollination services. We sampled commercial bumble bee colonies for the presence of two common gut parasites (Crithidia spp. and Apicystis bombi), and monitored bee pollination efficiency in tomato greenhouses exposed to an array of pesticides. The relationship between parasite prevalence and pesticide application differed by parasite species, and class of pesticide predicted pollination efficiency. Additionally, we found that bumble bee colony wax contained residues of pesticides not reported as having been sprayed during the experimental timeframe, suggesting that pesticide application in the greenhouse may not be as controlled as previously thought. Moving forward, our research will focus on automated monitoring of bumble bees in greenhouse systems, to better track foraging patterns.