Well-being plays a crucial role in the completion of PhD studies. However, recent research suggests that the components of universities' environment affect PhD students' well-being differently, resulting in various outcomes. This research explores the well-being of PhD students, constructed as a series of latent profiles, and assesses their associations with the impact of COVID-19 restrictions and student satisfaction with a PhD programme in a research-intensive university. Drawn from an ecological system perspective, students with similar patterns of PhD well-being were identified through latent profile analysis. Among 208 Russian participants, we established four well-being profiles: 'Disrupted well-being' (20.2%), 'Confident well-being' (28.8%), 'Dominated by Health and Research concerns' (26.9%) and 'Dominated by social connections concern' (24.1%) groups. The 'disrupted' group reported poor well-being regarding five out of seven domains. These students are less satisfied with the PhD programme than other participants and demonstrate the strongest worries about career prospects and degree completion due to COVID-19. The 'confident well-being' group is the most sustainable and resilient, as these students report satisfaction with their studies, achieve excellent scores in well-being domains and have fewer concerns about the pandemic's effect on their studies and degree completion. This profile mostly consists of male students. Satisfaction with the PhD programme contributes to the membership in this most desirable well-being profile. The two remaining groups demonstrated various alarming patterns of well-being, dominated by either 'Health and Home' and 'Research' domains or the 'Social' domain. This paper proposes recommendations for PhD programme managers and universities.