An increasing number of wild bee species are declining or threatened with extinction worldwide. Decline has been proposed to be caused by a combination of threats, including increasing wild bee disease prevalence and pathogen spillover from managed bees that can reduce health of wild bees. Most approaches aiming at characterizing bee health, 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 present a non-destructive protocol to collect bumble bee faeces and assess parasite loads of wild-caught individuals. The standard protocol consists of net-capturing individual bumble bees and placing them in a 10 cm (diameter) petri dish to collect faeces. This fecal screening approach is frequently used in laboratory settings, but much less in the field, which can impair conservation research. When placing bumble bees in a previously refrigerated cooler, we successfully collected faeces for 86% individuals, while the standard protocol, as used in laboratory settings, yielded 76% success in collecting faeces. We also identified cells and spores of two common gut parasites Crithidia spp. and Vairimorpha spp. in faecal samples. The faecal sampling presented here opens future avenues to assess bee pathogen loads using molecular techniques, while collected faeces could also be used to assess bee health more broadly, including bee microbiota and bee diet.