Abstract Objective This study tested whether exposure to minority stress and structural stigma across multiple levels of the family system were associated with two indicators of well‐being (life satisfaction, depressive symptoms) in LGBTQ+ parents across 19 European countries. Background Minority stress (i.e., identity‐based stress resulting from systemic oppression) and structural stigma (i.e., hostile legal environments, prejudicial social attitudes) are heterogeneous, yet well‐documented risk factors of reduced well‐being within LGBTQ+ populations. However, a comprehensive assessment stratifying both concepts across multiple levels of the family system (i.e., the individual, couple, and family level) is lacking for LGBTQ+ parents. Method Using data from the EU LGBTI Survey 2019, a sample of 3808 LGBTQ+ parents from 19 European countries was analyzed. Associations between self‐reported minority stress indicators, objective structural stigma indicators, sociodemographic predictors, and well‐being were tested using non‐linear, machine learning‐based techniques (gradient boosted decision tree models). Results Supporting preregistered hypotheses, exposure to individual‐level minority stress and individual‐ and family‐level structural stigma predicted life satisfaction and depressive symptoms. Couple‐level minority stress predicted life satisfaction, but not depressive symptoms, and family‐level minority stress predicted neither. Trans parents and those facing economic burdens were particularly vulnerable to low well‐being. Conclusions Exposure to minority stress and structural stigma, particularly within highly stigmatizing regions, are risk factors for LGBTQ+ parents' well‐being. Future research should examine the role of family‐level minority stress using validated measures.