Bee-pollen is an important source of nutritional and bioactive compounds. Given its high moisture content, bee-pollen is dried before commercialization; however, there are some drawbacks in the microbiological quality, which have a remarkable effect on the physicochemical stability. The aim of this study was to evaluate the influence of drying on bee-pollen at temperatures between 40 °C and 60 °C based on microbiological, structural and physical-chemical characteristics. The obtained results showed that bee-pollen dried at 40 and 50 °C had a significant increase in acidity after treatment, possibly due to the remain microbiological load. In contrast, a significant increase in flavonoids, phenolics and antioxidant activity was found for all thermal treatments; nonetheless, a loss of carotenoids by the effect of temperature was also obtained. Microscopy images showed a slight degradation in the bee-pollen structure, which may have caused the release of bioactive compounds, increasing the antioxidant capacity. A total ranking technique suggested the most adequate temperature for drying bee-pollen at 60 °C.