Wild bees are declining worldwide, and many species are now threatened with extinction. Decline is caused by a combination of threats, including disease spillover from managed bees that reduces health of wild bees. An increasing number of studies thus aim to characterize bee health. The common approaches, however, require sacrificing tens to hundreds of individual bees per site or species, with reports of several thousand individuals collected per study. Considering the widespread need to assess bee health, this sampling approach is not sustainable, especially for endangered populations or species. Here, we propose a non-destructive method to assess parasite loads of wild-caught bumble bees. The standard protocol consists of net-capturing individual bumble bees and placing them in a 10 cm (diameter) petri dish to collect faeces. Although this approach is frequently used in laboratory settings, it is not in the field, because of the low success in collecting faeces. Placing bumble bees in a previously refrigerated cooler, we significantly improved faecal collection in the field from 76% with the standard protocol to 86% with the cooler protocol. We also successfully identified spores and cells of two common gut parasites Crithidia spp. and Vairimorpha spp. in faecal samples. The efficacy of the cooler protocol, combined to the low-cost and widespread availability of the equipment should promote its use in field studies. Implication for insect conservation: As there are calls to reduce destructive sampling methods in bee research, using the updated cooler protocol will contribute to achieving this goal. This opens future avenues of combining this non-destructive approach to assess bee health with molecular tools.