Background: Excessive protein eating habits may cause kidney and liver disease and increase the risk of cardiovascular disease leading to incapacitation of the pilot. The purpose of this study was to identify sociodemographic and other factors on protein eating habits among civilian pilots in Indonesia. Methods: A cross-sectional study using secondary data from the survey of eating, drinking and physical exercise habits among civilian pilots in Indonesia 2016. Data collected were demographic characteristics, physical exercise habits, smoking habits, knowledge, body mass index and flight characteristics. Cox regression analysis was used to analyze the dominant factors associated with protein eating habits. Results: Among 528 pilots aged 19-64 years, 194 (36.74%) pilots had excessive protein eating habits . Long working period and body mass index were the dominant risk factors associated with protein eating habit in pilots. Compared to pilots with 1-9 years working period, pilots with 10-40 years working period had 35% lower risk of excessive protein eating habits (RRA = 0.65; 95% CI 0:49 - 0.87). Compared to pilots with normal body mass index, overweight pilots had 34% lower risk of excessive protein eating habits (RRA = 0.66; 95% CI 0:47 - 0.93). Conclusion: Long working period and overweight were protective factors from the risk of excessive protein eating habits