Ensuring a balance between training demands and recovery during basic military training (BMT) is necessary for avoiding maladaptive training responses (e.g., illness or injury). These can lead to delays in training completion and to training attrition. Previously identified predictors of injury and attrition during BMT include demographic and performance data, which are typically collected at a single time point. The aim of this study was to determine individual risk factors for injury and training delays from a suite of measures collected across BMT. A total of 46 male and female recruits undertaking the 12-week Australian Army BMT course consented to this study. Injury, illness, attrition, and demographic data were collected across BMT. Objective measures included salivary cortisol and testosterone, step counts, cardiorespiratory fitness, and muscular endurance. Perceptions of well-being, recovery, workload, fatigue, and sleep were assessed with questionnaires. Baseline and mean scores across BMT were evaluated as predictors of injury and attrition using generalized linear regressions, while repeated-measures ANOVA was used for the group comparisons. From the 46 recruits, 36 recruits completed BMT on time; 10 were delayed in completion or discharged. Multiple risk factors for injury during BMT included higher subjective ratings of training load, fatigue, and stress, lower sleep quality, and higher cortisol concentrations. Higher ratings of depression, anxiety, and stress, and more injuries were associated with a higher risk of delayed completion. Higher concentrations of testosterone and higher levels of fitness upon entry to BMT were associated with reduced risk of injury and delayed completion of BMT. Ongoing monitoring with a suite of easily administered measures may have utility in forewarning risk of training maladaptation in recruits and may complement strategies to address previously identified demographic and performance-based risk factors to mitigate injury, training delays, and attrition.