This study aims to evaluate differences in the risk factors for biochemical recurrence (BCR) for radical prostatectomy stratified by degree of obesity, focusing on the surgical method used. All 3099 patients who underwent radical prostatectomy in two medical centres from January 2008 to March 2018 were retrospectively reviewed. Patients were divided into three groups based on body mass index: ‘normal’, ‘overweight’, and ‘obese’. Risk factors associated with biochemical recurrence were compared between different degrees of obesity. We analysed the contributing risk factors of BCR-free survival using univariate and multivariable Cox hazard models. There were 378 (12.2%) and 1815 (58.6%) patients in the ‘obese’ and ‘overweight’ groups, respectively. Accordingly, 1324 patients underwent retropubic radical prostatectomy (RRP), and 1775 underwent robotic-assisted laparoscopic prostatectomy (RALP). Multivariable analysis showed that patients who underwent RALP had significantly lower BCR free survival in the ‘overweight’ and ‘obese’ groups than those who underwent RRP, with adjusted hazard ratios of 0.75 (95% CI 0.59–0.95, p-value = 0.01) and 0.55 (95% CI 0.33–0.90, p-value = 0.02), respectively. The degree of obesity was not directly associated with BCR-free survival. Robotic prostatectomy showed greater benefits in BCR-free survival than open prostatectomy in the ‘overweight’ and ‘obese’ groups.