The recovery of value-added compounds from agro-industrial by-products represents a sustainable strategy for developing novel functional ingredients. Berry seed oils, often discarded during fruit processing, are rich in bioactive lipids and may represent promising natural antibiofilm agents for controlling biofilm-forming bacteria relevant to food safety and public health. This study comparatively investigated the fatty acid composition of blackcurrant (Ribes nigrum) and raspberry (Rubus idaeus) seed oils and evaluated their effects on the metabolic activity of sessile cells in immature and mature bacterial biofilms. Fatty acid profiles were determined by GC–MS, while the metabolic activity of sessile cells was evaluated by the MTT reduction assay against immature (MTT0) and mature (MTT24) biofilms formed by Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Listeria monocytogenes, Pseudomonas aeruginosa, and Staphylococcus aureus. Oils were tested at 5 and 10 μL/mL. Blackcurrant seed oil contained high proportions of α-linolenic (21.37%), linoleic (46.45%), and oleic acids (16.44%), whereas raspberry seed oil was enriched in linoleic (59.72%) and oleic acids (22.86%) and lacked detectable α-linolenic acid. Despite these compositional differences, both oils reduced the metabolic activity of sessile cells, particularly at 10 μL/mL. In immature biofilms, blackcurrant seed oil showed the greatest reduction in sessile-cell metabolic activity against L. monocytogenes (58.00%), S. aureus (58.52%), and P. aeruginosa (57.50%), whereas raspberry seed oil was more effective against E. coli (42.34%) and K. pneumoniae (43.13%). In mature biofilms, raspberry seed oil reduced sessile-cell metabolic activity by up to 54.46% against L. monocytogenes, whereas blackcurrant seed oil achieved reductions of 46.69% against K. pneumoniae and 37.41% against A. baumannii. These findings support the sustainable valorization of berry-processing by-products and identify berry seed oils as promising natural antibiofilm agents for food biopreservation strategies aimed at reducing biofilm-associated microbial persistence.