Persistent inflammation and infection, often linked to staphylococcal colonization, affect bone-anchored hearing system (BAHS) outcomes. Although antibiotics are often used to treat skin complications, the roles of biofilms and antimicrobial resistance (AMR) in clinical success remain unclear. This clinical prospective study characterized biofilm formation and antibiotic resistance in Staphylococcus spp. from BAHS patients, and examined associations with inflammation, pain, and hygiene. Adults eligible for BAHS were prospectively enrolled at a tertiary university hospital in Sweden during 2014-2015. Fifteen patients were followed clinically and microbiologically at surgery, 3- and 12- months. Abutment, peri-abutment exudate and soft-tissue samples were cultured. Fifty-seven Staphylococcus spp. isolates underwent biofilm phenotyping (Crystal Violet, Congo Red), antimicrobial susceptibility testing (minimum inhibitory concentration [MIC], minimum biofilm eradication concentration [MBEC]) and whole-genome sequencing (lineage, AMR and virulence genes). Clinical status was scored (Holgers, pain, debris). Individual patients harbored the same staphylococcal clone on abutment, exudate, and tissue for 12 months. S. aureus was more prevalent in patients with inflammation (Holgers score >0), S. epidermidis correlated with pain, and slime production was associated with debris accumulation. Overall, 56 % of isolates showed resistance to fusidic acid, and 11-34 % carried tetracycline resistance genes. S. epidermidis carried multidrug resistance genes (beta-lactams, tetracycline, sulfamethoxazole, fosfomycin), and resistance increased under biofilm conditions (MBEC > MIC). The ica operon was detected in all S. aureus and S. epidermidis ST7, ST297, ST749 and ST278. These findings indicate that staphylococci from BAHS exhibit persistent colonization, diverse clonal lineages, and high biofilm-associated AMR. Early microbial diagnostics and biofilm-targeted strategies, alongside cautious use of topical antibiotics, may improve outcomes.