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Background Cigarette smoking among adults in the USA is a leading cause of preventable death worldwide, even though there has been a decline in prevalence since 2005. The addictive nature of nicotine is the chief reason smokers continue to use tobacco. Although the majority of smokers report a desire to quit smoking, a small minority who attempt to quit achieve long-term cessation. Combined, smoking cessation best practices include coordinated medication and behavioral treatments. However, these treatments are not currently adequately delivered to Medi-Cal beneficiaries in the publicly funded patient-centered medical homes (PCMHs) and community mental health clinics operated by Los Angeles County (LAC)-Department of Health Services (LACDHS) and LAC-Department of Mental Health (LACDMH). Methods This is a 5-year implementation, cluster-randomized comparative effectiveness trial that will support the implementation of smoking cessation services delivered in LAC-LACDHS-operated outpatient primary care clinics and in LAC-LACDMH-operated community mental health clinics. We will enroll 1000 participants from clinics that will offer smoking cessation services and 200 from clinics that will offer treatment as usual. Participants will be asked to complete assessments at baseline, 3 months, 6 months, and 12 months. The assessments will include self-reports on smoking history, anxiety, stress, quality of life, and participant satisfaction. Participants who are assigned to clinics that provide smoking cessation services will also be asked about the frequency of their participation in the smoking cessation services during the 12-month period. Discussion This study will evaluate the effectiveness and feasibility of implementing smoking cessation services in outpatient primary care and community mental health clinics. It will also determine if there will be higher rates of smoking cessation in the implementation sites as compared to the sites with treatment as usual. If the implementation proves to be effective, the plan is to sustain these services using a workflow we will develop in the LAC-operated sites. This would lead to ameliorating the significant smoking cessation treatment gaps among those served within the LAC Health Agency departments. Trial registration ClinicalTrials.gov NCT04717544 “Embedding comprehensive smoking cessation programs into community clinics.” Registered on January 22, 2021