Abstract Background This study assessed health workers’ adherence to neonatal health protocols before and during the implementation of a mobile health (mHealth) clinical decision-making support system (mCDMSS) that sought to bridge access to neonatal health protocol gap in a low-resource setting. Methods We performed a cross-sectional document review within two purposively selected clusters (one poorly-resourced and one well-resourced), from each arm of a cluster-randomized trial at two different time points: before and during the trial. The total trial consisted of 16 clusters randomized into 8 intervention and 8 control clusters to assess the impact of an mCDMSS on neonatal mortality in Ghana. We evaluated health workers’ adherence (expressed as percentages) to birth asphyxia, neonatal jaundice and cord sepsis protocols by reviewing medical records of neonatal in-patients using a checklist. Differences in adherence to neonatal health protocols within and between the study arms were assessed using Wilcoxon rank-sum and permutation tests for each morbidity type. In addition, we tracked concurrent neonatal health improvement activities in the clusters during the 18-month intervention period. Results In the intervention arm, mean adherence was 35.2% (SD = 5.8%) and 43.6% (SD = 27.5%) for asphyxia; 25.0% (SD = 14.8%) and 39.3% (SD = 27.7%) for jaundice; 52.0% (SD = 11.0%) and 75.0% (SD = 21.2%) for cord sepsis protocols in the pre-intervention and intervention periods respectively. In the control arm, mean adherence was 52.9% (SD = 16.4%) and 74.5% (SD = 14.7%) for asphyxia; 45.1% (SD = 12.8%) and 64.6% (SD = 8.2%) for jaundice; 53.8% (SD = 16.0%) and 60.8% (SD = 11.7%) for cord sepsis protocols in the pre-intervention and intervention periods respectively. We observed nonsignificant improvement in protocol adherence in the intervention clusters but significant improvement in protocol adherence in the control clusters. There were 2 concurrent neonatal health improvement activities in the intervention clusters and over 12 in the control clusters during the intervention period. Conclusion Whether mHealth interventions can improve adherence to neonatal health protocols in low-resource settings cannot be ascertained by this study. Neonatal health improvement activities are however likely to improve protocol adherence. Future mHealth evaluations of protocol adherence must account for other concurrent interventions in study contexts.