Background: Integrated healthcare delivered by work groups in nontraditional service settings is increasingly common, yet contemporary implementation frameworks typically assume a single organization--or organizational unit--within which system-level processes influence service quality and implementation success. Recent implementation frameworks predict that "inter-organizational alignment" (i.e., similarity in values, characteristics, activities related to implementation across organizations) may facilitate the implementation of evidence-based practices (EBP), but few studies have evaluated this premise. This study's aims examine the impact of overlapping organizational contexts by evaluating the implementation contexts of externally employed mental health clinicians working in schools--the most common integrated service delivery setting for children and adolescents. Aim 1 is to estimate the effects of unique intra-organizational implementation contexts and combined inter-organizational alignment on implementation outcomes. Aim 2 is to examine the underlying mechanisms through which inter-organizational alignment facilitates or hinders EBP implementation. Methods/design: This study will conduct sequential, exploratory mixed-methods research to evaluate the intra- and inter-organizational implementation contexts of schools and the external community-based organizations that most often employ school-based mental health clinicians, as they relate to mental health EBP implementation. Aim 1 will involve quantitative surveys with school-based, externally-employed mental health clinicians, their supervisors, and proximal school-employed staff (total n = 120 participants) to estimate the effects of each organization's general and implementation-specific organizational factors (e.g., climate, leadership) on implementation outcomes (fidelity, acceptability, appropriateness) and assess the moderating role of the degree of clinician embeddedness in the school setting. Aim 2 will explore the mechanisms through which inter-organizational alignment influences implementation outcomes by presenting the results of Aim 1 surveys to school-based clinicians (n = 30) and conducting semi-structured qualitative interviews. Qualitative data will be evaluated using an integrative inductive and deductive approach. Discussion: The study aims are expected to identify intra- and inter-organizational constructs that are most instrumental to EBP implementation success in school-based integrated care settings and illuminate mechanisms that may account for the influence of inter-organizational alignment. In addition to improving school-based mental health, these findings will spur future implementation science that considers the relationships across organizations and optimize the capacity of implementation science to guide practice in increasingly complex systems of care.