We assessed the effects of a three-year national-level, ministry-led health information system (HIS) data quality intervention and identified associated health facility factors. Monthly summary HIS data concordance between a gold standard data quality audit and routine HIS data was assessed in 26 health facilities in Sofala Province, Mozambique across four indicators (outpatient consults, institutional births, firstantenatal care visits, and third dose of diphtheria, pertussis, and tetanusvaccination) and five levels of health systemdata aggregation (daily facility paperregisters, monthly paper facility reports, monthly paper district reports, monthly electronic district reports, and monthly electronic provincial reports) through retrospective yearly audits conducted July-August 20102013. We used mixed-effects linear models to quantify changes in data quality over time and associated health system determinants. Median concordance increased from 56.3% during the baseline period (20092010) to 87.5% during 20122013. Concordance improved by 1.0% (confidence interval [CI] 0.60, 1.5) per month during the intervention period of 20102011 and 1.6% (CI 0.89, 2.2) per month from 20112012. No significant improvements were observed from 20092010 (during baseline period) or 20122013. Facilities with more technical staff (aß 0.71; CI 0.14, 1.3), more firstantenatal care visits (aß 3.3; CI 0.43, 6.2), and fewer clinic beds (aß -0.94; CI −1.7, −0.20) showed more improvements. Compared to facilities with no stock-outs, facilities with five essential drugs stocked out had 51.7% (CI −64.8 -38.6) lower data concordance. A data quality intervention was associated with significant improvements in health information system data concordance across public-sector health facilities in rural and urban Mozambique. Concordance was higher at those facilities with more human resources for health and was associated with fewer clinic-level stock-outs of essential medicines. Increased investments should be made in data audit and feedback activities alongside targeted efforts to improve HIS data in low- and middle-income countries.