Nowadays, bee products are commended by consumers for their medicinal and dietary properties. This study aimed to differentiate between monofloral bee pollens originating from Portugal using phenolic and volatile profiles and investigate their antioxidant and cytotoxic activity. Total phenolic and flavonoid compounds were recorded between 2.9–35.8 mg GAE/g and 0.7–4.8 mg QE/g, respectively. The LC/DAD/ESI-MSn analytical results allowed us to identify and quantify a total of 72 compounds, including phenolic and phenylamide compounds, whereas GC-MS results revealed the presence of 49 different compounds, mostly ketones, aldehydes, esters, hydrocarbons, and terpenes. The highest DPPH• radical scavenging activity, EC50: 0.07 mg/mL, was recorded in the sample dominated by Castanae sp. pollen, whereas the Rubus sp. (1.59 mM Trolox/mg) and Cistaceae sp. (0.09 mg GAE/g) pollen species exhibited the highest antioxidant activity in ABTS•+ and reducing power assays, respectively. Regarding the anti-carcinogenic activity, only Carduus sp. showed remarkable cytotoxic potential against MCF-7.