The objective of this study is to estimate the association between patient-initiated e-messages and quality of care among patients with diabetes and hypertension. In March 2011, the medical group eliminated a $60/year patient user fee for e-messaging and established a provider payment of $3–5 per patient-initiated e-message. Quality of care for patients initiating e-messages was compared before and after March 2011, relative to nonmessaging patients. Propensity score weighting accounted for differences between e-messaging and nonmessaging patients in generalized estimating equations. The study results show that patient-initiated e-messaging may increase the likelihood of completing recommended tests, but may not be sufficient to improve clinical outcomes for most patients with diabetes or hypertension without additional interventions.