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Abstract Background Improving the extent to which evidence-based practices (EBPs)—treatments that have been empirically shown to be efficacious or effective—are integrated within routine practice is a well-documented challenge across numerous areas of health. In 2014, the National Institute on Drug Abuse funded a type 2 effectiveness–implementation hybrid trial titled the substance abuse treatment to HIV Care (SAT2HIV) Project. Aim 1 of the SAT2HIV Project tests the effectiveness of a motivational interviewing-based brief intervention (MIBI) for substance use as an adjunct to usual care within AIDS service organizations (ASOs) as part of its MIBI Experiment. Aim 2 of the SAT2HIV Project tests the effectiveness of implementation and sustainment facilitation (ISF) as an adjunct to the Addiction Technology Transfer Center (ATTC) model for training staff in motivational interviewing as part of its ISF Experiment. The current paper describes the study protocol for the ISF Experiment. Methods Using a cluster randomized design, case management and leadership staff from 39 ASOs across the United States were randomized to receive either the ATTC strategy (control condition) or the ATTC + ISF strategy (experimental condition). The ATTC strategy is staff-focused and includes 10 discrete strategies (e.g., provide centralized technical assistance, conduct educational meetings, provide ongoing consultation). The ISF strategy is organization-focused and includes seven discrete strategies (e.g., use an implementation advisor, organize implementation team meetings, conduct cyclical small tests of change). Building upon the exploration–preparation–implementation–sustainment (EPIS) framework, the effectiveness of the ISF strategy is examined via three staff-level measures: (1) time-to-proficiency (i.e., preparation phase outcome), (2) implementation effectiveness (i.e., implementation phase outcome), and (3) level of sustainment (i.e., sustainment phase outcome). Discussion Although not without limitations, the ISF experiment has several strengths: a highly rigorous design (randomized, hypothesis-driven), high-need setting (ASOs), large sample size (39 ASOs), large geographic representation (23 states and the District of Columbia), and testing along multiple phases of the EPIS continuum (preparation, implementation, and sustainment). Thus, study findings will significantly improve generalizable knowledge regarding the best preparation, implementation, and sustainment strategies for advancing EBPs along the EPIS continuum. Moreover, increasing ASO’s capacity to address substance use may improve the HIV Care Continuum. Trial registration ClinicalTrials.gov: NCT03120598.