Bee-collected pollen (BCP) can serve as an excellent enhancer of functional food bioactivity, particularly when it is fermented. The aim of this study was to prepare a novel kombucha-based beverage (KPE) enriched with fermented monofloral rapeseed ( L.) BCP. To characterize the obtained samples, a proximate phytochemical composition analysis (including total phenolic and flavonoid content) was performed, as well as a detailed untargeted UHPLC-Q-ToF-MS profiling of phenolics and phenylamides. To biologically characterize KPE, antioxidant and antimicrobial activities were monitored. The total phenolic and flavonoid content, enhanced by the addition of BCP to the kombucha green tea beverage, was dose-dependent. The control sample showed a strong predominance of flavan-3-ols, distinguishing it from the KPE samples, where flavonol predominance and an increased content of phenolic acids were observed. Notably, the most significant markers of BCP were phenylamides, which were completely absent in the control. Although antioxidant activity was proximately highest in the control sample, KPE samples exhibited significantly improved antimicrobial activity.