Unhealthy behaviors may contribute to the development and the progression of chronic diseases with negative consequences on patients’ quality of life. The present study aimed to investigate the relationship between unhealthy behaviors (physical inactivity, tobacco consumption, and alcohol consumption) and health-related quality of life, measured with the SF-36 questionnaire, in women with endometriosis. To achieve this, data from a previous cross-sectional web survey among Italian adult women were analyzed. A total of 1045 responses were included in the analysis. Among the SF-36 subscales, the lowest score was recorded in the energy/fatigue domain: mean = 35.536 (Standard Deviation = 18.452). Smoking and physically inactive women had lower scores than non-smoking and physically active women, respectively, in each SF-36 domain. Women who drank more than one unit of alcohol a day, on average, reported lower scores than women with an alcohol intake <1 unit a day, for the following SF-36 domains: role limitations due to physical health, role limitations due to emotional problems, and emotional well-being. The multivariable analysis evidenced that employment, physical inactivity, and tobacco consumption were significant predictors for each SF-36 domain (p < 0.05). Physical inactivity and tobacco consumption had negative effects on the SF-36 subscales. Our results showed the need to monitor unhealthy behaviors to improve the overall well-being of women with endometriosis. Tailored strategies addressing smoking cessation, promoting physical activity, and moderating alcohol intake may aid in enhancing health-related quality of life in this vulnerable population.