The growth and development of a honey bee colony fundamentally rely on proper nutrition, leading beekeepers to nourish their hives to maintain the health and productivity of their colonies. Nevertheless, the substances utilized in honey bee nutrition vary widely, necessitating thorough research to evaluate their effects on the performance and health of honey bees. Herein, the supplemental diets commonly used by beekeepers for feeding bee colonies including soybean (Glycine max), maize pollen grains (Zea mays L), and a mixture of soybean and pollen grains, in addition to sugar solution as control group are evaluated. This study was conducted on both intestinal tissues as the main place of digestion and absorption and royal jelly (RJ) proteins as a final product that reflects physiological reactions within the insect’s body. Soybean has been observed to have detrimental effects on both the health of the intestinal tissue, causing atrophy of the epithelial cells and weakening of the stomach muscles. Additionally, a decrease in the secretory vesicles (SV) and the gelatinous layer (GL) within the intestine was noted. However, when honey bee colonies were fed on pollen, it helped maintain the molecular balance and high molecular weight proteins in RJ. Bee pollen diet also resulted in an increased production of SV. Conversely, feeding honey bees a mixture of soybean and pollen had catastrophic effects on both the intestinal tissue and RJ proteins. It also led to coagulation in the peritrophic membrane (PMb), which is crucial for protecting the intestinal walls and performing other physiological functions. This, in turn, impacted the absorption of proteins, the levels of SV, and GL. Consequently, it is suggested to incorporate bee pollen as a dietary supplement in the feeding plan of honey bees.