The aim of this study was to examine the effect of a supervised 6-week detraining period on bone metabolism markers, and their association with ergometrics, and components of the hypothalamic-pituitary-gonadal (HPG) axis in elite male professional soccer players. Sixty-seven soccer players (mean age ± SD 23.4 ± 5.2 years) that were following a supervised training program participated in this study. Players were tested twice: immediately after the conclusion of the competition period, and following the detraining period, for the determination of bone-turnover rates, ergometrics, and components of the HPG-axis. The detraining period resulted in significant reduction in osteocalcin [OC] (p < 0.001), C-terminal propeptide of collagen type-I [CICP] (p = 0.002), and bone-alkaline-phosphatase [b-ALP] (p < 0.001) values, while C-terminal telopeptide [CTX] was increased (p < 0.001). No significant relationships were apparent between bone biomarkers and body weight, body-fat %, total testosterone, free testosterone, estradiol, follicle-stimulating hormone, and luteinizing hormone in both experimental sessions (p > 0.05). Similarly, despite the deterioration in ergometrics after detraining (all p < 0.001), no significant correlations were evident (p > 0.05) between bone biomarkers and maximal oxygen consumption, squat jump, countermovement jump, and 20 m sprint performance, and also between % change of bone biomarkers and ergometrics, apart from a weak relationship (p = 0.041) between OC and VO2max of questionable value. Our results suggest that the 6-week soccer off-season detraining period in our study negatively affected bone physiology as reflected by the suppression of bone-formation rate and a parallel induction of bone resorption. The cause of this acute alteration of bone-turnover rates is not related to the examined components of the HPG-axis, although parallels is not associated with the changes in ergometrics.