Background Academic research has the potential to generate substantial benefits for society and the environment, yet systemic challenges—including precarious working conditions, pressures undermining research integrity, and barriers to accessible research—constrain its ability to do so. Existing initiatives have made valuable progress in improving research environments, but often remain fragmented responses that address individual symptoms rather than underlying systemic conditions. Meanwhile, contemporary research systems increasingly promote expectations for holistic research practice. This study argues that these broader aspirations provide a useful lens for understanding how research is shaped by its wider environment, and that meaningful improvement requires examining how they are applied in practice. Methods We conducted 34 semi-structured interviews with researchers at the University of York, a research-intensive UK university. Using a constructivist grounded theory approach, we explored researchers’ experiences across the Seven Dimensions of Holistic Research Practice: decolonising research methods; equity, diversity and inclusion; evaluation; impact; interdisciplinarity; responsible research and innovation; and working with external partnerships. These dimensions operationalised research aspirations as ‘work-as-imagined’, providing a lens for examining their relationship with ‘work-as-done’. Findings Four interconnected systemic tensions shaped the enactment of holistic research practice: friction arising from practical constraints; contradiction arising from competing definitions of research value; alienation arising from historically embedded academic norms; and starvation arising from insufficient capability development. Together, these tensions explain why work-as-imagined and work-as-done remain misaligned. Conclusions Building on these findings, this study develops the Systemic Realignment Framework as both a diagnostic and intervention framework, using the four systemic tensions to explain the conditions generating misalignment and identifying coordinated action across practice, institutional, and system levels through which it may be progressively reduced. Addressing these systemic challenges can support the meaningful enactment of holistic research practice, helping academic research better realise its potential and improving the experiences of those involved in the research process.