Background: Undocumented migrants live and work in precarious conditions. Few studies have explored the mental health consequences of such environment. The objective of this study is to describe the mental health of migrants at different stages of a regularization program. Methods: This cross-sectional study included migrants undocumented or in the process of regularization. We screened for symptoms of anxiety, depression and sleep disturbance using validated tools. We created a composite outcome of altered mental health including these components plus self-report of a recent diagnosis of mental health condition by a health professional. Results We enrolled 456 participants of whom 246 (53.9%) were undocumented. They were predominantly women (71.9%) with a median age of 43.3 (interquartile range: 15.5) years, from Latin America (63.6%) or Asia (20.2%) who had lived in Switzerland for 12 (IQR: 7) years. Overall, 57.2% presented symptoms of altered mental health. Prevalence of symptoms of anxiety, depression and sleep disturbance were 36% (95% confidence interval: 31.6–40.6%), 45.4% (95% CI: 40.8–50.1%) and 23% (95% CI: 19.2–27.2), respectively. Younger age (adjusted odd ratio: 0.7; 95% CI: 0.5–0.9 for each additional decade), social isolation (aOR: 2.4; 95% CI: 1.4–4.2), exposure to abuse (aOR: 1.9; 95% CI: 1.1–3.5), financial instability (aOR: 2.2; 95% CI: 1.4–3.7) and multi-morbidity (aOR: 3.2; 95% CI: 1.7–6.5) were associated with increased risk of having altered mental health while being in the early stages of the process of regularization had no effect (aOR: 1.3: 95% CI: 0.8–2.2). Conclusions This study highlights the need for multi-pronged social and health interventions addressing the various domains of undocumented migrants living difficulties as complement to legal status regularization policies. Protection against unfair working conditions and abuse, access to adequate housing, promoting social integration and preventive interventions to tackle the early occurrence of chronic diseases may all contribute to reduce the burden of altered mental health in this group. More research is needed to assess the long-term impact of legal status regularization on mental health.