Influenza vaccination is underused. We examined changes in vaccination following decision support and workflow changes in a cross-sectional analysis of three vaccination seasons among adult primary care patients from 21 practices. Interventions included clinical decision support changes to facilitate documentation; changes to rooming workflow for medical assistants and licensed practical nurses to promote vaccination, prepare orders, document care done elsewhere; and record patient refusals. We measured rates for a national vaccination performance measure and receipt of onsite vaccination. Approximately 120,000 patients were eligible each season. Performance on the quality measure increased each year (40.6% to 62.5% to 76.4%). Corresponding rates of onsite vaccination were 27.7%, 28.8%, and 31.5%. The adjusted odds ratio for onsite vaccination in the second season compared with the first was 0.94 (95% confidence interval [CI] 0.92, 0.96). Onsite vaccination was more likely in the third season compared with either previous season-adjusted odds ratio for third versus second 1.14 (95% CI, 1.12, 1.16) or adjusted odds ratio for third versus first 1.07 (95% CI 1.05-1.09). Sequential changes in decision support and patient rooming process workflows were associated with large improvements in measured performance and with a significant increase in clinic-administered influenza vaccination by the third season.