This study aimed to evaluate the physical, chemical, and microbiological characteristics of bee-collected pollen, with special consideration to the antimicrobial resistance of the isolated microorganisms to the selected antibiotics. A hierarchy cluster analysis was conducted, in which bee pollen samples were divided into four groups by their colour. The highest antioxidant activity among monofloral bee pollen was found for the autumn raspberry pollen and the lowest for the clover pollen, using the ABTS test. The total phenol content in rapeseed bee pollen was the second-highest among all samples analysed, which might indicate a correlation between high phenol content and strong antioxidant activity. Our study indicated a moderate correlation between bee pollen moisture content and Enterobacteriaceae counts, as well as a correlation between moisture content and total bacterial count. Among all bacteria (n = 34) isolated from pollen, the highest prevalence was found in Bacillus spp. and coagulase-negative staphylococci. The resistance of isolated microorganisms was identified in 18 cases. The high number of antimicrobial resistance cases, i.e., when isolates were resistant to ampicillin (seven cases) and penicillin (eight cases), indicates an environmental effect because, for this study, no antibiotics were used in the apiaries harvesting pollen. This indicates the need for improved safety procedures in bee pollen production for human consumption.