Bee pollen (BP) is a natural product with remarkable nutritional and bioactive composition. Some of the compounds of interest are carotenoids with provitamin A activity, possessing an excellent antioxidant capacity and positive health effects. For that, the objective of this work was to characterize the botanical origin and carotenoid profile in two particle sizes of Colombian BP by Rapid Resolution Liquid Chromatography (RRLC). The carotenoid profile and α-tocopherol content were obtained, and ANOVA analysis was employed to explore data. The main carotenoids found were 9Z-zeaxanthin (65.15 ± 7.41–1104.98 ± 113.41 μg/g pollen), zeaxanthin (35.29 ± 2.08–354.30 ± 29.91 μg/g pollen), two zeaxanthin isomers (18.23 ± 3.73–227.69 ± 19.00 μg/g pollen) and β-cryptoxanthin (8.67 ± 1.27–34.25 ± 2.25 μg/g pollen). The statistical analysis showed significant differences between harvest time and particle size, proving the influence of climatic and botanic factors. The high content of macular and provitamin carotenoids was highlighted, which proposes BP as a significant source of important bioactive compounds. The carotenoids found allows characterizing BP in a complete seasonal cycle (January–December), research conducted for the first time in this product. Also, the information reported can be used to select harvest time of BP in order to include it as an ingredient, supplement, or raw material in the food industry, according to the carotenoid composition needed.