Few studies have evaluated eating disorders in military personnel engaged in defense activities during the COVID-19 pandemic. We aimed to determine the prevalence and factors associated with eating disorders in military personnel from Lambayeque, Peru. A secondary data analysis was performed among 510 military personnel during the second epidemic wave of COVID-19 in Peru. We used the Eating Attitudes Test (EAT-26) to assess eating disorders. We explored associations with insomnia, food insecurity, physical activity, resilience, fear to COVID-19, burnout syndrome, anxiety, depression, post-traumatic stress and selected sociodemographic variables. Eating disorders were experienced by 10.2% of participants. A higher prevalence of eating disorders was associated with having 7 to 12 months (PR: 2.97; 95% CI: 1.24–7.11) and 19 months or more (PR: 2.62; 95% CI: 1.11–6.17) working in the first line of defense against COVID-19, fear of COVID-19 (PR: 2.20; 95% CI: 1.26–3.85), burnout syndrome (PR: 3.73; 95% CI: 1.90–7.33) and post-traumatic stress (PR: 2.97; 95% CI: 1.13–7.83). A low prevalence of eating disorders was found in the military personnel. However, prevention of this problem should be focused on at-risk groups that experience mental health burdens.