The objective of this analysis was to evaluate the effect of resident program training size on clinician productivity and turnover in the Veterans Health Administration (VHA), the largest education and training platform for medical professionals in the United States. We retrieved administrative data on training programs and training facilities from the VA Office of Academic Affiliations and the VHA Corporate Data Warehouse. Data on primary care physician shortage areas were retrieved from the Health Resources and Services Administration. We used a quasi-experimental instrumental variables 2SLS design and constructed an exogenous predicted training allocation treatment variable as a function of the total national training program allocation. The outcome was clinical staff productivity and turnover. Secondary analyses stratified results using Health Professional Shortage Areas data (HPSA). Data were obtained for a national dataset of 141 VHA medical facilities and 26 specialties that hosted training programs across 11 years from 2011 to 2021 (N = 132,177). Instrumental variables results showed that on average, an increase of one training slot in a specialty leads to a decrease of 0.039 visits per standardized clinic day (p < 0.001) and a 0.02 percentage point increase in turnover (p < 0.001). The direction of this association varied by specialty: while psychiatry and psychology specialties saw a decline in productivity, fields such as primary care and cardiology experienced an increase in productivity. HPSA stratified results indicate that negative effects on productivity and turnover are driven by areas with little to no primary care physician shortage, whereas shortage areas experienced a small increase in productivity and no effect on turnover. This quasi-experimental evaluation indicates that resident training program size is associated with reduced productivity and increased turnover in specialties such as psychiatry and in facilities with high baseline productivity. However, in specialties like primary care and cardiology, as well as areas with shortages of primary care, larger training programs are associated with increased productivity.