We conducted a longitudinal examination to assess the relationship between lifestyle habits, including exercise habits, and the incidence of undernutrition after the Great East Japan Earthquake in March 2011. Of the 31,411 participants aged ≥60 years who lived in the municipalities’ evacuation areas before the disaster and had undergone health examinations, 17,622 persons with a body mass index of 20–25 kg/m2 were followed up through the FY 2017 (a mean follow-up of 6.9 years). The analysis involved 13,378 individuals who could be followed. The associations between undernutrition after the disaster and lifestyle factors were estimated via multivariable-adjusted analysis using the Cox proportional hazard regression model. The dependent variable was the proportion of undernutrition after the disaster, whereas independent variables included evacuation, exercise habits/physical activity, alcohol consumption, smoking, meals before bedtime, gastrointestinal surgery history, history of lifestyle-related diseases, and two or more subjective symptoms. In total, 1712 of the 13,378 participants were newly undernourished after the disaster. The statistically significant variables influencing the occurrence of undernutrition were non-evacuation (hazard ratio (HR), 1.31; 95% confidence index (CI) 1.17–1.47), poor exercise habits (HR, 1.14; 95% CI 1.03–1.50), and poor physical activity (HR, 1.12; 95% CI 1.01–1.25). Other significant related variables were drinking habits, surgical history, lifestyle-related diseases, and two or more subjective symptoms. These results suggest that regular exercise and/or physical activity might be important in preventing undernutrition following a disaster, regardless of sex, other lifestyle habits, or past medical history.