Integrative medicine (IM) is a clinical paradigm of whole person healthcare that combines appropriate conventional and complementary medicine (CM) treatments. Studies of integrative healthcare systems and theory-driven evaluations of IM practice models need to be undertaken. Two health services research methods can strengthen the validity of IM healthcare studies, practice theory, and fidelity evaluation. The University of Arizona Integrative Health Center (UAIHC) is a membership-supported integrative primary care clinic in Phoenix, AZ. A comparative effectiveness evaluation is being conducted to assess its clinical and cost outcomes. A process evaluation of the clinic's practice theory components assesses model fidelity for four purposes: (1) as a measure of intervention integrity to determine whether the practice model was delivered as intended; (2) to describe an integrative primary care clinic model as it is being developed and refined; (3) as potential covariates in the outcomes analyses, to assist in interpretation of findings, and for external validity and replication; and (4) to provide feedback for needed corrections and improvements of clinic operations over time. This paper provides a rationale for the use of practice theory and fidelity evaluation in studies of integrative practices and describes the approach and protocol used in fidelity evaluation of the UAIHC.