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Abstract Poor quality maternal and neonatal healthcare contributes to preventable deaths, birth complications, and long-term health disabilities. Organizational factors have a significant contribution for key maternal and neonatal health indicators improvement. A facility-based pre–post interventional evaluation design was deployed. Package of interventions were implemented in a phased approach. The study was conducted in three regions in Ethiopia. A total of 131 health facilities were included in the study. A mixed-Poisson regression models were used to examine the predictors to identify organizational factors. Quality improvement practice results were measured using improved clinical bundles, and maternal and neonatal health quality indicators. One hundred three(78.6%) and 117(89.3%) health facilities had at least one improved clinical bundle and MNH quality indicators, respectively. Team work, client satisfaction survey and a quality structure with clear terms of reference were found to be predictors of improved clinical bundle indicators with an incidence rate of 1.87(95% CI [1.06, 3.29), 1.27(95% CI [1.12, 1.44]) and 1.34(95% CI [1.23, 1.47]) respectively. The cross-level interaction model revealed that health facilities implementing all three interventions (customer survey*teamwork*quality structure showed the strongest effects of 3.55(95% CI [2.53, 5.00]) times better outcomes verses facilities with none of them. On the other hand, knowledge on quality improvement, health facilities being hospital, resistance to change and staff turnover were found to be predictors of improved MNH quality indicators with an incidence rate of 1.34(95% CI [1.08, 1.67]), 1.35(95% CI [1.08, 1.67]), 0.73(95% [0.58, 0.92]) and 0.62(95% [0.50, 0.76]) respectively. Improved clinical bundles were linked to teamwork, a culture of conducting customer feedback and having a quality structure with clear terms of reference. Improved MNH quality indicators were associated with health facility type, quality improvement knowledge, acknowledgment of staff resistance and staff turnover. Program implementers should prioritize these critical organizational factors while applying quality initiatives.