The use of dietary supplements is popular among military personnel. However, there is a lack of understanding about the changes in use during deployment and the specific factors associated with such changes. This study retrospectively examined changes in the pattern of supplement use among Australian veterans during their deployment to Iraq (n = 8848) and Afghanistan (n = 6507) between 2001 and 2009 and identified work-related circumstances that were associated with these changes. The frequency of use of supplements at present and during deployment was assessed. Multiple logistic regression analysis was used to compare the use of supplements among different groups and among those with different deployment experiences. The study found that overall use of supplements was highest on deployment to Afghanistan (27.8%) compared with deployment to Iraq (22.0%, p < 0.001) or after deployment (current use, 21.2%; p < 0.001). Personnel who were younger or who were at the rank of noncommissioned officer were more likely to use dietary supplements. Men were more likely to use body-building supplements, whereas women more often used weight-loss supplements. Those veterans who did not report using supplements regularly on deployment were far less likely to use them subsequently. Combat exposure, mixed duty cycles, and working long hours during deployment were associated with higher supplement use. The findings confirmed that supplement use in the military reflects the unique demands and stressors of defence service.