Bariatric surgery remains the most efficacious method to produce long term weight-loss and to reduce comorbidities associated with severe obesity. Despite extensive research on how it impacts weight outcomes, changes in food cravings and cognition around food before and after bariatric surgery are an underexplored topic. We report an ongoing attempt to measure changes in the dynamic patterns of food cravings and food-related cognitions before and after bariatric surgery using Ecological Momentary Assessment (EMA) in a sample of women with a prior history of Binge Eating Disorder. This ongoing study also aims to assess dietary intake, sleep, and physical activity. Data collection methods include two 7-day protocols (before and after bariatric surgery), each consisting of eight EMA prompts delivered daily through text messages using questions from the General Food Cravings Questionnaire-State (G-FCQ-S), seven 24-hour food recalls (ASA-24), and daily use of an activity and sleep monitor. With an initial aim of recruiting ten participants, only eight out of thirty participants who were either screened or started the study protocol completed it over two years since the start of the study. Despite abundant access to patients due to partnering with a local bariatric surgery center, we have faced significant barriers to participant enrollment and completion. Reasons for ineligibility or failure to complete study protocols included participant drop-out from the bariatric surgery program (due to personal reasons, not meeting insurance requirements or timelines, or not meeting the pre-surgical cardiometabolic health requirements), insufficient completion rates of 24-hour food recalls, failure to activate the text-messaging service for the EMA protocol, and inability to respond to eight EMA prompts per day due to work schedule restrictions. The two-part protocol and the population of choice (bariatric surgery candidates) resulted in a much lower enrollment and completion rate than that of a similar week-long study conducted in our laboratory with women attending a binge-eating disorder support group, in which 14 participants out of 21 screened completed the study. The lessons learned from this project should help other researchers conducting longitudinal EMA studies with multiple phases and multiple data collection instruments to plan for the challenges of participant recruitment, follow-up, and adherence to study protocols.