Background: Proper nutrition has a positive impact on health. Paradoxically, excessive preoccupation with healthy eating may lead to the emergence of abnormal eating behaviours and increase the risk of developing disorders. The aim of this study was to assess the risk of orthorexia (ON) and the prevalence of emotional eating (EE) in military flying personnel of the Polish Air Force in relation to BMI and sociodemographic factors. Methods: This study included 760 soldiers (including 60 females) taking part in the National Health Programme 2021–2025. The ORTO-15 questionnaire and EEQ were used to assess the risk of ON and EE. Results: The risk of ON occurred in 28.9% of military flying personnel and was significantly more frequent in soldiers with a normal weight (46.4%), under 40 years of age (42.7%), and with higher education (42.7%). The prevalence of EE was found in approximately 12.3% of the respondents and was significantly more common in soldiers with diagnosed obesity (17.5%), women (21.7%), and soldiers with higher education (13.6). Other sociodemographic variables did not differentiate the results of the ORTO-15 questionnaire and EEQ. Conclusions: The obtained results indicate that the problem of eating disorders also occurs in military populations. The necessity of continuing research in this area is discussed.