Purpose International and Australian guidelines on the management of diabetes-related foot infections, recommend proximal bone analysis to guide post-operative antibiotic therapy in patients undergoing foot amputations. Despite observational evidence suggesting correlation between histopathology and clinical outcomes, routine histopathology is rarely performed in Australia, perhaps due to turnaround time and controversy around the inter-rater agreement among pathologists. We studied the concordance between histopathology and microbiology in this cohort. Methodology A single-centre retrospective, study between January 2023 and February 2024 at Sir Charles Gairdner Hospital, Perth included diabetic patients ≥18 years, who underwent below ankle amputation with histopathological analysis from proximal bone samples. Secondary outcomes were rate of revision surgery, subsequent antibiotic therapy, readmission to hospital, and persistent infection at 3- and 6-months post-amputation. Results Sixty-seven patients were included of whom 51 (76%) were male, with mean age 66 years. Whilst 31% of samples demonstrated pathological inflammation, microbiological growth was detected in 70% resulting in only 53% concordance. Mean reporting time for histopathology was 11 days. At 3-months 19% of cases had had revision surgery, 27% received subsequent antibiotic therapy, 22% were readmitted to hospital, and 16% had signs of persistent infection. Six-month data collection is ongoing. Conclusions This study highlights the high rate of discordance between histopathology and microbiology from proximal bone samples in diabetes-related foot infections and in adverse outcomes following amputation. Further studies are needed to investigate the optimal approach to determine residual infection post-surgery, duration of antibiotic therapy and optimal prevention of adverse outcomes.