Subchondral bone injury is prevalent in racehorses at sites subjected to high magnitude cyclic loading such as the palmar aspect of the condyles of the third metacarpal bone. Therefore these injuries are thought to occur due to bone material fatigue, when microdamage accumulates at a rate higher than can be repaired through bone remodelling. Understanding the accumulation of subchondral bone microdamage will help to develop management strategies aimed at reducing the occurrence of subchondral bone fractures. The aim of this study was to determine the association of racehorse training history and bone microstructure with the accumulation of microdamage in the subchondral bone. The medial metacarpal condyles from 46 horses (26 in race training and 20 resting after a period of training), and their racing history, were obtained. Bone microdamage was assessed by grading microCT images and by quantifying subchondral bone microcracks on bulk-stained bone blocks. Explanatory variables with associations in univariable models were selected for inclusion in multivariable logistic and linear regression models and retained if P < 0.05. Higher grades of microdamage were associated with increasing career duration (OR 2.19; P < 0.001) and lower bone mineral density (OR 0.96; P = 0.012). Similarly, higher microcrack density was associated with increasing career duration (Coef. 0.13; P = 0.004), with being in training rather than resting at the time of sampling (Coef. 0.35; P = 0.015), and with higher bone volume fraction (Coef. 4.45; P < 0.001). These results show that bone microdamage in the metacarpal condyles accumulates throughout a horse’s racing career despite some reduction during rest periods, and is not consistently associated with inferior bone microstructural properties. Therefore management strategies such as reducing the intensity and the duration of training periods are likely to have the greatest impact on prevention of subchondral bone injury in racehorses.