This dataset contains nanoLC-MS/MS results of heads of honey bee workers. All the heads were from 13 days old bees that were 11 days postinfection (DPI) that lasted 24 hours. Abdomens of bees were analyzed using qPCR to determine parasite load. Further, corresponding selected heads were subjected to a label-free proteomic analysis. Overall, five heads of bees were selected from each of the following experimental exposures performed: i) control without L. passim and IMI exposure and with confirmed no L. passim detected; ii) bees positive for L. passim from the experimental exposure of L. passim; and iii) bees positive for L. passim from the experimental exposure of L. passim combined with 2.5 uL IMI coexposure. This research was supported by project no. QK1910018 (NAZV) and Institutional Support for R&D no. MZE-RO0423 of the Ministry of Agriculture of the Czech Republic.