Blackberries, and berries in general, were an essential part of the human diet until the Neolithic. Fruits from Rubus species are among the richest food source of ellagitannins, anthocyanins, and flavonoids, all phenolic compounds quite scarce in the typical western diet. After ingestion, most of these bioactive compounds have a relatively low bioavailability but they can impact positively the health of the gastrointestinal tract and be metabolized by gut microbiota. The microbial derivatives are much more bioavailable than their precursors and can act at systemic level various days after ingestion and accumulate in some vital organs. The diversity of microbial derivatives and their relative concentrations depend on the metabolic capabilities of each individual microbiota. Bioavailable compounds from blackberries and main microbial derivatives of ellagitannins and anthocyanins show important protective effect and potent bioactivity against some chronical diseases.