Abstract Background Little is known about the prevalence of non-communicable diseases (NCDs) among newly arrived refugees in Europe and whether their medical needs are met. The objective of this study was to investigate patterns of NCDs as refugee claimants migrate, whether refugee claimants experience unmet healthcare needs before, during and after flight when living in Greek refugee camps and to elucidate sociodemographic determinants for unmet medical care needs in the Greek refugee camps. Methods Survey data collected in 2016 among 267 newly arrived adult asylum-seekers staying at six refugee camps in Greece was used. The survey was available in English, Arabic and Farsi. We inspected frequency distributions of NCDs and unmet medical care needs, and using multiple logistic regression analysis, we estimated determinants for unmet medical needs in Greece. Results The majority had a good or fair self-reported health; yet, 17.1% suffered from 1 NCD, while 42.1% suffered from 2 or more NCDs. The most prevalent reported NCDs in Greece were: back or neck pain (26.6%) and severe headache (24.7%). The prevalence of most NCDs in the migration phases followed a U- or J-shaped pattern: decreased during migration and increased after migration to Greece. Unmet medical care needs were reported by 41.3% with one NCD after arrival in Greece. Compared with young adults, adults aged 51+ years were in increased risk of reporting unmet medical needs in Greece [odds ratio = 7.59; p = 0.015]. Conclusions The high number of persons who report NCDs underscore the need for availability of diagnostic tools and agents to ensure that the refugee claimants receive the right healthcare assistance. Tools and guidelines to provide continuity of NCD care when people migrate are likewise important. Many European countries that receive this group of refugees should take the disease patterns, including multi-morbidity, into consideration when planning for health reception and the organization of healthcare. Key messages The prevalence of NCDs among refugee claimants decreased during migration and increased after migration to Greece. Unmet medical care needs were reported by 41.3% with one NCD after arrival in Greece.