Background The rapid adoption of electronic record systems to support patient care in dental practice provides an opportunity for the development of technology-driven clinical decision support (CDS) applications. The purpose of this study was to understand how a CDS tool integrated into existing electronic dental record (EDR) software was used by practicing dental hygienists and dentists in the process of assessing and addressing patients’ tobacco use and referring them to outside tobacco cessation resources. Methods Employing a user-centered design methodology over the course of 8 days, researchers observed dental providers’ use of a tobacco CDS tool during encounters with patients who smoke cigarettes. Using a process called contextual inquiry, they observed 11 dental hygiene patient encounters during 4 visits to 4 different general dental clinics. Semi-structured interviews were conducted with 22 HealthPartners Dental Group dental staff, including dental hygienists, dental assistants, and dentists. Dental hygienists were found to be the primary users of the CDS tool and were surveyed on satisfaction with the usefulness and ease of operating the CDS tool. A thematic analysis of the observation and survey data was undertaken. Results The tobacco cessation CDS tool was used by most dental hygienists but few dentists involved in the care of patients who use tobacco. Interruptions to workflow were categorized as “breakdowns” and were found to be infrequent but in some cases meaningful. In some instances, hygienists reported that the tool allowed more accurate and detailed information to inform their clinical decision-making as well as better documentation of patients’ nicotine dependence level and interest in quitting. A minority reported patient dissatisfaction, though patient reports and observations did not confirm these impressions. Negotiations about rules regarding which provider(s) were responsible for tobacco assessment, messaging, and documentation as well as the frequency with which tobacco use should be assessed and discussed had not been resolved consistently. Conclusions Findings suggest that user-centered design of a CDS tool can support more consistent assessment and documentation of tobacco use and the delivery of evidence-based, personalized quit messaging targeted to and acceptable by patients.