Background: The use of ecological momentary assessment (EMA) to study youth experiencing homelessness (YEH) behaviors is an emerging area of research. Despite high rates of participation and potential clinical utility, few studies have investigated the acceptability and recommendations for EMA from the YEH perspective. Objective: This study aimed to describe the perceived benefits, usability, acceptability, and barriers to the use of EMA from the homeless youth perspective. Methods: YEH were recruited from a larger EMA study. Semi-structured exit interviews were performed using an interview guide that focused on the YEH experience with the EMA app and included perceived barriers and recommendations for future studies. Data analyses used an inductive approach with thematic analysis to identify major themes and subthemes. Results: A total of 18 YEH aged 19-24 years participated in individual and group exit interviews. The EMA was highly acceptable to YEH and they found the app and EMA surveys easy to navigate. Perceived benefits included increased behavioral and emotional awareness with some YEH reporting a decrease in their high-risk behaviors as a result of participation. Another significant perceived benefit was the ability to use the phones for social support and make connections to family, friends, and potential employers. Barriers were primarily survey and technology related. Survey-related barriers included the redundancy of questions, the lack of customizable responses, and the timing of survey prompts. Technology-related barriers included the “freezing” of the app, battery charge, and connectivity issues. Recommendations for future studies included the need to provide real-time mental health support for symptomatic youth, to create individually customized questions, and to test the use of personalized motivational messages that respond to the EMA data in real time. Conclusions: YEH are highly receptive to the use of EMA in studies. Further studies are warranted to understand the impact of EMA on YEH behaviors. Incorporating the YEH perspective into the design and implementation of EMA studies may help minimize barriers, increase acceptability, and improve participation rates in this hard-to-reach, disconnected population.