Honey bee colony performance and health are intimately linked to the foraging environment. Recent evidence suggests that the US Conservation Reserve Program (CRP) has a positive impact on environmental suitability for supporting honey bee apiaries. However, relatively little is known about the influence of habitat conservation efforts on honey bee colony health. Identifying specific factors that influence bee health at the colony level incorporates longitudinal monitoring of physiology across diverse environments. Using a pooled-sampling method to overcome individual variation, we monitored colony-level molecular biomarkers during critical pre- and post-winter time points. Major categories of colony health (nutrition, oxidative stress resistance, and immunity) were impacted by apiary site. In general, apiaries within foraging distance of CRP lands showed improved performance and higher gene expression of vitellogenin (vg), a nutritionally regulated protein with central storage and regulatory functions. Mirroring vg levels, gene transcripts encoding antioxidant enzymes and immune-related proteins were typically higher in colonies exposed to CRP environments. Our study highlights the potential of CRP lands to improve pollinator health and the utility of colony-level molecular diagnostics to assess environmental suitability for honey bees.