Sweet cherry (Prunus avium L.) is a tree widely cultivated in temperate regions for its tasty and healing fruits. Pruning works on the tree give each year considerable amounts of woody wastes that hardly have any utility. The aims of this work were to detect the most active antioxidants present in a cherry pruning wood sample, to isolate and characterize them, and study the antimicrobial and antibiofilm activities of components found in the wood ethyl acetate extract against a selection of foodborne microorganisms. The online HPLC–DPPH technique allowed the detection of two active antioxidant peaks that, after being isolated by a combination of countercurrent chromatography (FCPC) and conventional preparative techniques, and subsequent structural characterization by NMR, MS and polarimetry, resulted to be (‒)-catechin (1) and (‒)-taxifolin (4). Other components of the cherry wood extract were also isolated, among which compounds 1, 4, and (+)-dihydrowogonin (12) have never been reported in P. avium. A selection of the isolated flavonoids was submitted to antimicrobial and antibiofilm activity evaluations against strains from type culture collections, as well as on multi-resistant strains previously isolated in our laboratory. Those compounds with antimicrobial activity detected in preliminary screenings by standard agar diffusion tests ‒the flavan-3-ol 1, the flavanonols 4 and (+)-aromadendrin (5), the flavanone (+)-pinocembrin (15), and the flavone tectochrysin (17)‒ were subjected to the minimal inhibitory concentration (MIC) test, showing all of them MIC values of 100 μg/mL. Compound 4 also induced a significative inhibition on the formation of biofilms by Enterobacter sp. UJA37p at a concentration of 1 μg/mL and a significative disruption of preformed biofilm by this strain at 0.1 µg/mL. Similar results on biofilm disruption were observed with compound 17.