Integrating research-based treatments into clinical settings has become a priority in the substance abuse treatment field. This article examines the introduction of research, via manualized treatment (i.e., the Matrix Model), into community treatment settings that participated in the Center for Substance Abuse Treatment Methamphetamine Treatment Project, a multi-site randomized controlled trial (RCT) that provided free treatment to 1016 methamphetamine-dependent individuals. With both empirical (qualitative) and anecdotal data from those involved clinically in the project, the article utilizes the framework of practitioner concerns set forth by Addis, Wade, and Hatgis (1999) to assess the issues realized during the implementation of this manualized treatment. Despite fairly smooth implementation of the model, the authors conclude that introducing manualized treatment in the context of an RCT may not be the best way to bring research-based treatment into the practice world.