The group of innovative ingredients in cosmetic preparations includes bio-ferments (Bs), which are characterized by high bioactivity and biocompatibility, and one of the plants rich in bioactive compounds that has a beneficial effect on the skin and the body is Silybum marianum. Bio-ferments obtained from this plant are becoming increasingly useful as active ingredients in cosmetics. In the present study, four different bio-ferments were obtained by fermentation of pomace (B-P), extract (B-E), oil (B-O), and seeds (B-S) of milk thistle. Their biodegradability (%B), total polyphenols content (Folin–Ciocalteu method), and antimicrobial, antioxidant (DPPH, ABTS, and FRAP methods), chelating (Fe2+ ions), and reduction (Cu2+ and Fe3+ ions) properties, as well as the acidity, were evaluated. The contact angle using the sessile drop method was assessed to investigate bio-ferments’ impact on skin wettability. Finally, the content of selected phenolic acids in the Bs was evaluated using the HPLC method, while the lactic acid (LA) content was assessed using the GC-MS method. All bio-ferments were characterized by high polyphenols content (13.56 ± 0.10–15.28 ± 0.12 mmol GA/L B), chelating (0.08 ± 0.01–0.17 ± 0.01 mmol Fe2+/L B) and antioxidant activity (DPPH method, 2.41 ± 0.01–3.53 ± 0.01 mmol Tx/L B), and reducing Cu2+ and Fe3+ ions. Gallic acid, protocatechuic acid, caffeic acid, neochlorogenic acid, coumaric acid, and LA were identified in Bs. The most increased antibacterial activity for B-P was observed for a strain of Staphylococcus aureus (MIC = 250 μL/mL) and Pseudomonas aeruginosa (MIC = 250 μL/mL). Simultaneously, B-S demonstrated the highest inhibitory effects against Escherichia coli (MIC = 125 μL/mL), emphasizing the varied antimicrobial profiles of these bio-ferments against different bacterial strains. Research on aerobic biodegradation demonstrated a high level of degradation (%B= 60 ± 1–65 ± 3), and all Bs were categorized as readily degradable according to the OECD classification.