There are substantial concerns about impaired honey bee health and colony losses due to several poorly understood factors. We used MALDI profiling (MALDI BeeTyping®) analysis to investigate how some environmental and management factors were related to the haemolymph peptidome (all peptides in the circulatory fluid), which reflects the immune status of Apis mellifera, under field conditions across Europe. Honey bees were exposed to varying environmental stressors across eight European countries totalling 128 agricultural sites, reflecting two different crop systems [oilseed rape (OSR) and apple (APP)]. Molecular signatures of haemolymph and the presence/absence of molecular-related ions of three immunity markers, namely the antimicrobial peptides (AMP) Apidaecin, Abaecin and Defensin-1, allowed discrimination of bee responses by country, crop type and site. However, many sites showed no significant signature related to the presence of AMP markers. Conversely, in Sweden (SWE), molecular ion intensities were very high, including those of the AMP markers. Even the lowest values were always higher than in other countries. Furthermore, all experimental sites in SWE expressed AMPs. A machine learning model was developed to discriminate the haemolymphs of bees from APP and OSR sites. The model was 90.6% accurate in identifying the crop type from the samples used to build the model. Overall, MALDI BeeTyping® on individual bee haemolymph represents an attractive and promising “blood test” for monitoring the impact of stressors on bee health at the landscape scale, thus providing policymakers with new monitoring and regulatory tools.