Transcutaneous bone biopsy (TCB) is the gold standard for taking microbiological specimens in diabetic foot osteomyelitis (DFO), but this technique is not widely used in diabetic foot care centers. We aimed to evaluate the reliability of per-wound bone biopsy (PWB) cultures by comparing them with concomitant TCB cultures obtained through healthy skin. This is a prospective monocentric study including patients seen in consultation for clinical and radiological diabetic foot osteomyelitis with positive probe-bone tests between April 2015 and May 2018. Two bone biopsies were performed on each consenting patient: TCB through a cutaneous incision in healthy skin, and PWB, after careful debridement of the wound. A total of 46 paired cultures were available from 43 eligible patients. Overall, 16 (42%) of the PWB and TCB pairs had identical culture results, but the TCB cultures were sterile in 8 (17%) cases. For 38 paired cultures with positive TCB, the correlation between PWB results and TCB results was 58.4%. PWB revealed all microorganisms found in the transcutaneous specimen in 26/38 samples (68.5%). In patients with DFO, the culture results of specimens taken by per-wound biopsies did not correlate well with those obtained by TCB. PWB should be reserved for cases where the transcutaneous biopsy is sterile or not feasible.