This study aims to investigate (1) microbial patterns in fracture-related infections (FRIs) in comparison to microbiological patterns of periprosthetic joint infections (PJIs), (2) the identification of effective empiric antibiotic therapy for FRIs and PJIs and (3) analysis of difficult-to-treat (DTT) pathogens. Patients treated for FRIs or PJIs from 2017 to 2020 were evaluated for pathogens detected during treatment. Antibiotic susceptibility profiles were examined with respect to broadly used antibiotics and antibiotic combinations. Resistance rates to rifampicin or fluoroquinolone were determined. A total of 81 patients with PJI and 86 with FRI were included in the study. For FRIs Staphylococcus aureus was the most common infection-causing pathogen (37.4% vs. 27.9% for PJI). Overall, there was no statistical difference in pathogen distribution (p = 0.254). For FRIs, combinations of gentamicin + vancomycin (93.2%), co-amoxiclav + glycopeptide and meropenem + vancomycin (91.9% each) would have been effective for empiric therapy, similar to PJIs. Difficult to treat pathogens were more frequently detectable in PJIs (11.6% vs. 2.3%). Empiric therapy combinations such as gentamicin + vancomycin, co-amoxiclav + glycopeptide or meropenem + vancomycin, are effective antibiotic strategies for both FRI and PJI patients. More DTT pathogens were detectable in PJIs compared to FRIs.