Environment, forage quality, management practices, pathogens and pesticides influence honeybee responses to stressors. This study proposes an innovative approach to assess colony health and performance using molecular diagnostic tools, by correlating hemolymph proteins with common measures of colony strength, prevalent honeybee pathogens (Varroa destructor and Nosema spp.) and essential elements (iron, zinc and copper). Colonies were selected from four apiaries in the province of Bologna (Italy), located in different environmental and foraging conditions. Haemolymph samples were taken from June to October 2019. The Varroa infestation of the colonies was estimated by assessing the natural fall of the mites, while the bees were tested for Nosema spp. spores using microscopic method. Proteins were separated using SDS-PAGE and colony performance was assessed by determining adult bees, total brood, and honey and pollen reserves. The biomarkers measured proved to be useful for monitoring changes in performance and trophic conditions during summer and early autumn. Significant correlations were found between haemolymph proteins and colony performance measures. A positive correlation between pollen reserves and vitellogenin and hexamerin 70a highlights the importance of these proteins for successful overwintering. In October, Varroa infestation was negatively correlated with total proteins, vitellogenin, apolipophorin II, transferrin, and hexamerin 70a, with negative implications for overwintering; furthermore, Varroa infestation was also negatively correlated with iron content, potentially affecting iron homeostasis.