Background Ecological momentary assessment (EMA) is a promising data collection tool for mobile health interventions targeting episodic health behaviors. For substance-using men who have sex with men (SUMSM), EMA is becoming more widely utilized in efforts to characterize substance use and sexual risk factors for HIV transmission. However, recent literature demonstrates emerging concerns over compliance and lower EMA engagement and data concordance among racial and ethnic minority SUMSM. Objective This study aimed to provide a qualitative evaluation of the barriers and facilitators of EMA as a data collection tool among racial and ethnic minority SUMSM. Methods Between October and November 2017, 45 racial and ethnic minority SUMSM were recruited from a list of prior research participants at the San Francisco Department of Public Health to participate in daily EMA surveys on their substance use and sexual health behaviors for 1 week, followed by in-person focus groups (FGs). A total of 4 FGs explored the participants’ experiences with the surveys, issues regarding privacy and confidentiality, and suggestions for improvement. Qualitative analysis was performed using content analysis. Descriptive statistics and Fisher exact tests were used to assess the associations between demographics or substance use behaviors and EMA completion. Results Overall, 93.9% (295/314) of all delivered surveys were initiated, and of those, 98.0% (289/295) were completed. Neither participant demographics, including race ( P =.65) or age ( P =.43), nor substance use behaviors, including the frequency of alcohol ( P =.40) or methamphetamine ( P =.91) use or any cocaine ( P =.28), crack ( P =.99), or polysubstance use ( P =.24), were found to be associated with survey completion. Overall, participants were receptive to the text message–based EMA surveys. Facilitators included survey timing, user-friendly survey design, survey-stimulated self-reflection, coding of sensitive phrases, and other privacy benefits of a mobile survey. Barriers included an inability to correct texting errors and participants’ perception of judgment or stigmatization related to questions about condomless sex. To improve EMA compliance and uptake, participants suggested adding response confirmations, clarifying survey language, and continuing to diversify the study audience. Conclusions EMA appears to be feasible and acceptable among this sample of racial and ethnic minority SUMSM. Close attention to EMA study design and the development of nonjudgmental, contextualized questions regarding stigmatized health behaviors may be critical to further improve EMA compliance.