Honeybee pollen (HBP) is a mixture of floral pollen collected by honeybees near the hive. It is characterized by a composition rich in phenolic compounds, carotenoids and vitamins that act as free radicals scavengers, conferring antioxidant and antibacterial capacity to the matrix. These bioactive properties are related to the botanical origin of the honeybee pollen. Honeybee pollen samples were collected from different geographical locations in central Chile, and their total carotenoid content, polyphenols profile by HPLC/MS/MS, DPPH radical scavenging capacity, and antimicrobial capacity against S. pyogenes, E. coli, S. aureus, and P. auriginosa strains were evaluated. Our results showed a good carotenoids content and polyphenols composition, while antioxidant capacity presented values between 0–95 % for the scavenging effect related to the botanical origin of the samples. Inhibition diameter for the different strains presented less variability among the samples, Furthermore, binary mixtures representing the two most abundant species in each HBP were prepared to assess the synergy effect of the floral pollen (FP) present in the samples. Data shows an antagonist effect was observed when assessing the carotenoid content, and a synergy effect often presents for antimicrobial and antioxidant capacity for bee pollen samples. The bioactive capacities of the honeybee pollen and their synergy effect could apply to develop new functional ingredients for the food industry.