Increasing evidence on the effects of the COVID-19 pandemic suggests that its social and health impacts are being disproportionately shouldered by socioeconomically disadvantaged populations, including migrants. Knowledge of how these populations are experiencing the COVID-19 crisis is scarce. We examined the effects of the pandemic on the perceived individual financial situation and health condition of migrants in Lisbon, Portugal, and described the most affected subgroups. A cross-sectional survey was conducted with a diverse community-based sample of 1126 migrants. A worsening of their financial situation since the pandemic was reported by 55.6% of the participants and a worsening of their health condition by 19.9%. A worsened financial situation was most often reported by those ≥45 years old and with a lower income (<EUR 650). Likewise, a worsened health condition was most often reported by older and lower-income migrants, as well as by women and those with a lower level of education. Migration-related factors such as length of stay and migration status were not associated with worsened health conditions. Socioeconomic characteristics appear to be more important when assessing differences in perceived effects of the pandemic among migrants. The social impact of the pandemic both exacerbates economic and gender inequalities and may lead to worse health conditions within the population in the medium and long terms.