Background: Excessive mileage can be detrimental to bone mineral density among long-distance runners. The negative effects of mileage could be alleviated by appropriate nutrition. The purpose of this study was to analyse the dietary-lifestyle patterns in relation to bone mineral density and bone turnover markers among amateur marathoners. Methods: A total of 53 amateur male distance runners were divided into two clusters by k-means cluster analysis. Bone mineral density was measured by dual X-ray absorptiometry (DXA). Blood was drawn to analyse bone resorption marker C-terminal telopeptide (cTX) and bone formation marker amino-terminal propeptide of type I collagen (PINP). Food frequency intake and lifestyle information were measured by multicomponent questionnaire KomPAN®. Yearly average mileage per month was taken from each participant. Results: There were two distinguished clusters: Less-healthy-more-active-low-Z-score (LessHA) (n = 33) and More-healthy-less-active-high-Z-score (MoreHLA) (n = 20). LessHA had a lower frequency intake of pro-healthy food groups, a lower number of meals during a typical day, and a higher mileage training than the group of athletes who followed the MoreHLA. Athletes following the LessHA pattern also had a lower Z-score in the lumbar spine and femoral bone and a lower PINP. Conclusion: The current study suggests that pro-healthy dietary patterns and lower mileage may favour higher bone mineral density in male amateur marathoners.