Background There is a substantial body of literature that discusses the problematic nature of asylum seeker healthcare in several European countries. However, little is known about how asylum seekers experience primary healthcare in Malta. Aim This paper draws on a qualitative study that aimed to explore the nature of healthcare encounters between asylum seekers and healthcare professionals in Maltese primary healthcare and the contextual processes which influence these interactions. Methodology The study utilised critical ethnography, informed by postcolonial theory. Data were collected through observation of encounters between healthcare professionals and asylum seekers (130 hours) and in-depth interviews with asylum seekers ( n11), cultural mediators ( n4) and Maltese healthcare professionals ( n7). Results Thematic analysis of the combined data resulted in three themes: ‘the impact of seeking refuge’, ‘seeking mutual understanding’ and ‘seeking resolution’. Healthcare encounters between asylum seekers and professionals are characterised by ‘othering’ practices, pre-conceived expectations and mutual mistrust. These are shaped by a complex interplay of factors, including damaging experiences of migration, derogatory political and public discourses and inadequate resources. Conclusion In Maltese primary care, healthcare encounters are highly problematic for both patients and professionals. Nurses could take the lead in developing services to assess complex needs and aid asylum seekers in navigating the healthcare system.