Abstract Background Tobacco use remains the leading cause of death and disability in the USA and is disproportionately concentrated among low socioeconomic status (SES) populations. Community Health Centers (CHCs) are a key venue for reaching low SES populations with evidence-based tobacco cessation treatment such as Quitlines. Electronic health record (EHR)-based interventions at the point-of-care, text messaging (TM), and phone counseling have the potential to increase Quitline reach and are feasible to implement within CHCs. However, there is a lack of data to inform how, when, and in what combination these strategies should be implemented. The aims of this cluster-randomized trial are to evaluate multi-level implementation strategies to increase the Reach (i.e., proportion of tobacco-using patients who enroll in the Quitline) and Impact (i.e., Reach × Efficacy [efficacy is defined as the proportion of tobacco-using patients who enroll in Quitline treatment that successfully quit]) and to evaluate characteristics of healthcare system, providers, and patients that may influence tobacco-use outcomes. Methods This study is a multilevel, three-phase, Sequential Multiple Assignment Randomized Trial (SMART), conducted in CHCs (N = 33 clinics; N = 6000 patients). In the first phase, clinics will be randomized to two different EHR conditions. The second and third phases are patient-level randomizations based on prior treatment response. Patients who enroll in the Quitline receive no further interventions. In phase two, patients who are non-responders (i.e., patients who do not enroll in Quitline) will be randomized to receive either TM or continued-EHR. In phase three, patients in the TM condition who are non-responders will be randomized to receive either continued-TM or TM + phone coaching. Discussion This project will evaluate scalable, multi-level interventions to directly address strategic national priorities for reducing tobacco use and related disparities by increasing the Reach and Impact of evidence-based tobacco cessation interventions in low SES populations. Trial registration This trial was registered at ClinicalTrials.gov (NCT03900767) on April 4th, 2019.