Abstract Background Awareness of health disparities based on sexual orientation has increased in the past decades, and many official public health agencies throughout Europe call for programs addressing the specific needs of lesbian, gay and bisexual (LGB) individuals. However, the acceptance of LGB individuals varies significantly in different countries, which potentially influences health and well-being in this population. We explored differences in self-rated health and subjective well-being between individuals living in same-sex and opposite-sex couples. We also examined the effects of discrimination and country-level variations in LGB acceptance on health and well-being and the potential mediating role of social capital in these associations. Methods Using the 2010 European Social Survey ( n  = 50,781), 315 individuals living with a same-sex partner were matched and compared with an equal number of individuals living in opposite-sex couples. We performed structural equation modeling analyses to estimate path coefficients, mediations and interactions. Results LGB acceptance was significantly related to better self-rated health and subjective well-being among all individuals, and these associations were partially mediated by individual social capital. No differences in these associations were found between individuals living in same-sex and opposite-sex couples. Sexuality-based discrimination had an additional significantly negative effect on self-related health and subjective well-being. Conclusions The findings of this study suggest a negative association between exposure to discrimination based on sexual orientation and both health and well-being of individuals living in same-sex couples. Members of same-sex couples and opposite-sex couples alike may benefit from living in societies with a high level of LGB acceptance to promote better health and well-being.