An optimal learning climate is crucial for the quality of residency training and may also improve residents' well-being and empathy. We investigated the associations of learning climate with residents' work-related well-being. A multicenter questionnaire study was performed among 271 surgery and gynaecology residents in 21 training programs from September 2012 to February 2013. Residents were asked to complete work-related well-being measurements: work engagement (Utrecht Work Engagement Scale), job and specialty satisfaction (measures from Physician Worklife Study), and physician empathy (Jefferson Scale of Physician Empathy). The Dutch Residency Educational Climate Test was used to evaluate learning climate. Multivariate adjusted linear regression analyses were used to estimate associations of learning climate with work-related well-being measures. Well-being measures were completed by 144 residents (53.1%). Learning climate was evaluated by 193 residents, yielding 9.2 evaluations per training program on average. Overall learning climate score was positively associated with work engagement [regression coefficient b = 0.58; 95% confidence interval (CI) 0.18-0.98; p = 0.004] and job satisfaction (b = 0.80; 95% CI 0.48-1.13; p < 0.001). No associations were found between learning climate and empathy and specialty satisfaction. Residents' work engagement and job satisfaction are positively related to the learning climate and may be further enhanced by improved learning climates of training programs.