Animal-derived foods (ADF) are carriers of toxin-producing multidrug-resistant (MDR) S. aureus strains, posing a global food safety risk. We evaluated the toxin and biofilm production capabilities of S. aureus isolates from ADF marketed in Assam, India. Of the 138 staphylococcal isolates, 29 (21.01%) were identified as S. aureus, mostly isolated from raw milk. Resistance to chloramphenicol (13.79%), erythromycin (68.96%), penicillin (93.10%), enrofloxacin (20.68%), tetracycline (55.17%), trimethoprim-sulfamethoxazole (20.68%), linezolid (6.89%), cefoxitin (55.17%), and oxacillin (48.27%) was noted. Approximately 82.75% isolates were MDR, whereas 27.58% carried mecA gene, indicating methicillin-resistant S. aureus. PCR toxinotyping revealed pvl (20.69%), sea (37.93%), and sed (17%) genes. Additionally, 6.89% isolates harbored seb, sei, and tst genes; all lacked eta, etb, see, seg genes. A significant difference (P < 0.05) was observed in sea and sei genes across food sources. Biofilm-forming genes were detected as icaA (65.51%), icaB (34%), icaC (48.27%), icaD (27.58%), clfA (51.72%), clfB and fnbA (44.82%). At least one biofilm-associated gene was found in 72.41% of isolates, while two or more genes were present in 80.95%. Approximately 87.5% of mecA-positive isolates contained at least one biofilm-associated gene. A significant difference (P < 0.05) was noted in icaA, icaD, clfB, and fnbA across the different ADF sources.