Strawberry, raspberry, blueberry, and blackberry by-products were analyzed for proximate composition, bioactive compounds, antimicrobial activity, and fermentability by 13 potential probiotic strains. Proximate composition was assessed using AOAC methods and gas chromatography, individual phenolic compounds were quantified through UHPLC-PDA, and antimicrobial activity was determined using the broth microdilution technique. Berry bagasses were then added as carbon source in growth media, being alternatively washed to remove simple sugars, to evaluate the effect of the bagasse on microbial growth and enzymatic production through the API ZYM kit. Glucose and fructose levels ranged from 8.9 to 24.3 g/100 g dry weight, with minor amounts of sucrose and myo-inositol. Eighteen phenolics were quantified, with high amounts of ferulic acid, 4-hydroxybenzoic acid, cyanidin 3-glucoside, and petunidin 3-glucoside. Blackberry bagasse showed the highest pathogen inhibition (71.6–96.5%). Lacticaseibacillus rhamnosus GG and Lentilactobacillus kefiri BIOTEC014 succeeded on media with strawberry or blueberry bagasse as carbon source. The washing of strawberry and blueberry bagasses reduced growth (47–78%) but enhanced enzymatic activity, particularly β-glucosidase in BIOTEC014. These findings suggest that berry bagasses can serve as valuable functional ingredients for food and pharmaceutical applications.