In 2015, more than 1 million asylum seekers and refugees arrived in Europe. Information on how European countries addressed the prevention and control of infectious diseases among these populations during and after this period is limited. This study is based on 27 semi-structured interviews conducted with first-line staff and health officials in May–June 2016 in first-entry countries (Greece/Italy), transit countries (Croatia/Slovenia) and destination countries (Austria/Sweden). Characteristics of health-service provision for infectious diseases at each stage of reception, with a focus on tuberculosis, viral hepatitis, intestinal parasites and human immunodeficiency virus infections, were investigated. No major differences in the provision of services in accordance with migration status (asylum seekers vs refugees) were reported. At arrival, interventions were focused on addressing emerging health needs and no major barriers to accessing acute hospital care for infectious diseases were reported. There were shortcomings in interventions to tackle medium- to long-term needs with respect to infectious diseases, including screening for chronic treatable infections and adult vaccination. European evidence-based guidance highlighting the most relevant interventions for infectious diseases during the reception process is needed.