Honey bees play a crucial role in agricultural production. Farmers rely on commercial bee pollination to obtain optimal yields, and beekeepers on the income from pollination fees. However, commercial pollination confronts honey bees with pests and pathogens, pesticides, and low-quality food, which in many cases do not fulfill the minimal nutritional requirements of honey bees. In this work, we evaluated honey bee nutrition in avocado and blueberry plantations under organic and conventional management, by assessing the nutritional quality of pollen and bee bread based on their protein, fatty acid, and microbial content, and by analyzing honey bee health through the examination of abdominal fatty acid profiles and head protein content. Low protein content in honey bee hemolymph was evident under conventional management. Regardless of management, avocado pollen showed higher protein levels, which were translated into higher honey bee head protein levels being 60% higher in avocado under conventional management when compared to blueberry under the same management. However, higher protein levels in avocado pollen were also translated into lower amounts of fatty acids in bee bread and in honey bee fat. In particular, the total amount of fatty acids in bee bread from conventional management was 50% lower than that from organic management. Additionally, the saturated fatty acids in conventional blueberries were lower compared to that of organic blueberries. Crop system and bee bread microbial composition altered the plant-honey bee nutrition cascades transforming pollen to bee bread with increased amount of saturated, unsaturated, and total fatty acids. In conclusion, both crop species and crop systems determine honey bee nutrition through alterations in the pollen transformation, affecting protein and fatty acid assimilation.