This investigation delves into radio frequency (RF) drying as a novel approach for preserving the inherent quality and extending shelf life of lotus bee pollen, a primary agricultural product enriched with essential nutrients and bioactive compounds. Through a comparative analysis with conventional hot air (HA) drying conducted at 50 °C, 55 °C, and 60 °C, this study evaluated the impact of both drying techniques on critical quality parameters of bee pollen. These parameters included moisture content, fatty acid profile, color, aroma characteristics, pigment concentrations, and malondialdehyde levels. Findings revealed that RF drying significantly reduced drying time while maintaining superior quality attributes of bee pollen, such as enhanced color retention (ΔE < 5) and diminished lipid oxidation, in comparison to HA drying. Notably, RF drying at 55 °C for 130 min emerged as the optimum condition for preserving the sensory and nutritional qualities of lotus bee pollen. The study underscores the potential of RF drying as an efficient and quality-preserving method that could be advantageous for commercial applications in food industry, aiming at enhancing shelf life and safety of bee pollen.