Objectives: to describe the association between personal and organisational value discrepancies and compassion ability, burnout, job satisfaction, absenteeism, and consideration of early retirement among healthcare professionals. Design: online cross-sectional survey. Setting: primary, secondary, and tertiary care. Participants: 1025 current practising clinicians (doctors, nurses, and allied health professionals) in Aotearoa/New Zealand. Main outcome measures: The Sinclair Compassion Questionnaire - Healthcare Provider Ability and Competence Self-Assessment, The Maslach Burnout Inventory - Human Services Survey abbreviated 2-Question Summative Score, 10-item Warr-Cook-Wall Job Satisfaction questionnaire, measures of absenteeism and consideration of early retirement. Results: Perceived discrepancies between personal and organisational values predicted lower compassion ability (B =-0.006, 95% CI [-0.01, -0.00], P<0.001, f2=0.05) but not competence (p=0.24), lower job satisfaction (B =-0.20, 95% CI [-0.23, -0.17], P<0.001, f2=0.14), higher burnout (B =0.02, 95% CI [0.01, 0.03], P<0.001, f2=0.06), absenteeism (B =0.004, 95% CI [0.00, 0.01], P=0.01 f2=0.01), and greater consideration of early retirement (B =0.02, 95% CI [0.00, 0.03], P=0.04, f2=0.004). Conclusions: Working in value-discrepant environments predicts a range of poorer outcomes among healthcare professionals, including the ability to be compassionate. Scalable organisational and systems level interventions that address operational processes and practices that lead to the experience of value discrepancies are recommended to improve clinician performance and wellbeing outcomes. Study registration: the study was pre-registered on AsPredicted (Registration number 75407)