Ayahuasca, a traditional Amazonian medicine, has shown promise for the treatment of substance use and other mental disorders. Takiwasi Center is an accredited Peruvian therapeutic community (TC) offering an ayahuasca-assisted addiction treatment program combining elements of traditional Amazonian medicine (e.g., plant diets, purges), individual and group therapies, and Catholic-based ritual. The Ayahuasca Treatment Outcome Project is a longitudinal mixed-methods evaluation of outcomes among inpatients who attended this residential program. Participants completed semi-structured interviews and a battery of validated measures including two baseline-only measures that assessed mental health comorbidity and treatment motivation. Outcome measures included the ASI (V5), BAI, BDI, and the WHOQOL-BREF, among others. Structured interviews were conducted at intake, during program, discharge, and at 3, 6, 12, and 24 months post-discharge. Interviews included several semi-structured questions as well as Likert rating scales to assess perceived usefulness of different aspects of the program and overall satisfaction. In this talk we discuss outcomes at 12 and 24 month follow-up, with attention to the methodological challenges of conducting research on a complex psychedelic-assisted substance use health intervention. In addition to methodological concerns, we address and reflect on the complicated role of researchers and our relationships with the clinical institutions that we study.