The aim of this study was to investigate the concordance between swab and tissue biopsy samples in terms of microbiological isolates and their time-related changes. A total of 156 samples (78 swab and 78 biopsy) were collected from 39 cases of partial- or full-thickness burns and compared at days 7 and 14 after admission regarding the type of microorganisms and their time-related changes. Pseudomonas aeruginosa and Citrobacter freundii were the two most common microorganisms found by both sampling methods. While the majority of swab and biopsy samples were concordant in day 7, the rate of concordance in day 14 was less than day 7—87.1% versus 66.6%, respectively. After comparing the ratio of P aeruginosa and C freundii in positive swab and biopsy cultures on days 7 and 14, unlike the swab samples, the biopsy samples yielded similar results both times (75% P aeruginosa and 25% C freundii, respectively). The results of this study show that the swab is a sufficient tool for burn wound monitoring during the first week and could defer the need for invasive biopsy sampling. For patients who remain in the burn unit for a longer period, biopsy samples are justified for monitoring the bacterial activity in burn wounds.