Background Mobile health (mHealth) is showing increasing potential to address health outcomes in underresourced settings as smartphone coverage increases. The NeoTree is an mHealth app codeveloped in Malawi to improve the quality of newborn care at the point of admission to neonatal units. When collecting vital demographic and clinical data, this interactive platform provides clinical decision support and training for the end users (health care professionals [HCPs]), according to evidence-based national and international guidelines. Objective This study aims to examine 1 month’s data collected using NeoTree in an outcome audit of babies admitted to a district-level neonatal nursery in Malawi and to demonstrate proof of concept of digital outcome audit data in this setting. Methods Using a phased approach over 1 month (November 21-December 19, 2016), frontline HCPs were trained and supported to use NeoTree to admit newborns. Discharge data were collected by the research team using a discharge form within NeoTree, called NeoDischarge. We conducted a descriptive analysis of the exported pseudoanonymized data and presented it to the newborn care department as a digital outcome audit. Results Of 191 total admissions, 134 (70.2%) admissions were completed using NeoTree, and 129 (67.5%) were exported and analyzed. Of 121 patients for whom outcome data were available, 102 (84.3%) were discharged alive. The overall case fatality rate was 93 per 1000 admitted babies. Prematurity with respiratory distress syndrome, birth asphyxia, and neonatal sepsis contributed to 25% (3/12), 58% (7/12), and 8% (1/12) of deaths, respectively. Data were more than 90% complete for all fields. Deaths may have been underreported because of phased implementation and some families of babies with imminent deaths self-discharging home. Detailed characterization of the data enabled departmental discussion of modifiable factors for quality improvement, for example, improved thermoregulation of infants. Conclusions This digital outcome audit demonstrates that data can be captured digitally at the bedside by HCPs in underresourced newborn facilities, and these data can contribute to a meaningful review of the quality of care, outcomes, and potential modifiable factors. Coverage may be improved during future implementation by streamlining the admission process to be solely via digital format. Our results present a new methodology for newborn audits in low-resource settings and are a proof of concept for a novel newborn data system in these settings.