Background: Responding to the mental health needs of refugees remains a pressing challenge worldwide. We estimated the prevalence of psychological distress in a large refugee population in Germany and assessed its association with host country factors amenable to policy intervention and integration indicators. Method: We analysed the second wave of the IAB-BAMF-SOEP, a representative Germany-wide survey of 2,639 adult refugees who arrived between 2013 and 2016, which included the Refugee Health Screener. Results: Almost half of the population surveyed (41.3%[95%-CI:37.9%-44.6%]) was affected by psychological distress. 10.9%(8.3%-13.4%) of the population screened positive for severe distress. Risk of distress was particularly high for women (53%[47.1%-58.9%]), older refugees (aged ≥55:70.4% [58.5%-82.2%]), Afghan nationals (61.2%[53.2%-69.2%]), individuals under threat of deportation (RR:1.54[1.13-2.1]), single males (1.41[1.09-1.82]), and those in collective housing (1.2[1.02-1.42]). Distressed males had a lower likelihood of employment (0.66[0.51-0.84]) and reduced participation in integration courses (0.9[0.81-1.01]). Affected females were less often in education (0.43[0.18-1.04]). Conclusions: The finding that a large minority of refugees in Germany exhibits distress calls for an expansion of mental health services for this population. Service providers and policy-makers should consider the increased risk among female, older and Afghan refugees, as well as among single men, residents in collective housing and those under threat of deportation. The associations between mental health and integration processes like labour market, educational program and integration course participation also warrant consideration.