Background Social connection throughout the life course is increasingly understood as critically important for mental and physical health. We sought to investigate the feasibility of using ecological momentary assessment (EMA) and wearable accelerometers to characterize the effects of social isolation and/or loneliness experienced by adolescents during the COVID-19 pandemic on their mental and physical health.Methods We recruited 19 participants ages 13–18 from an Adolescent Medicine practice in Atlanta, Georgia. Participants completed surveys at baseline regarding their degree of social isolation and loneliness, as well as their family functioning, school climate, social media use, and COVID-19 experiences. Participants reported on their social isolation, loneliness, social media use, and emotional state up to four times daily for the subsequent 2-week study period using EMA. We also requested participants wear an activity tracker and heart rate measurement device for 14 days to monitor their physical health. Participant feedback was collected via open-ended exit interviews. Feasibility of recruitment/retention, adherence, and exploratory outcome measures were investigated. The pre-specified progression criteria were a recruitment rate of > 30% and a retention rate of > 80%.Results Participants’ ages ranged from 14 to 18 years, and most (13 of 19) identified as female and as Black/African American (16 of 19). Progression criteria were met for recruitment of participants, but not retention. Only 6 participants returned the wearable devices. On average, participants contributed 12 days of EMA data and 8 days of activity tracker/heart rate data. In exploratory analyses, social isolation was correlated with lower school climate, higher COVID-19 experiences, higher depression scores, and lower sleep quality. Loneliness also showed correlation with all these factors except COVID-19 experiences.Conclusions Retention in a cohort study using EMA and wearable accelerometer use was not feasible in this population of adolescents recruited during the COVID-19 pandemic. Baseline survey data did reveal important correlates of social isolation and loneliness that should be explored in future studies. Future research should further partner with adolescents to design longitudinal studies that mitigate barriers related to the pandemic and other factors on subject recruitment and retention.