Background: Effective planning for disease prevention and control requires accurate, adequately-analysed, interpreted and communicated data. In recent years, efforts and investments have been put in strengthening health management information systems (HMIS) in Sub-Saharan Africa to improve data accessibility to decision-makers. This study assessed the quality of routine HMIS data at primary healthcare facility (HF) and district levels in Tanzania. Methods: The assessment involved Outpatient, Inpatient, Antenatal care, Family Planning, Post-natal care, Labour and Delivery, and Provider-initiated Testing and Counselling service areas in primary health care facilities. Records were tracked and compared at different phases of the data journey i.e. registers, tally-sheets, HF monthly reports submitted to the district level, and electronic database. We assessed the availability and utilization of each HMIS tool and quantified completeness and accuracy levels of the collected data in each phase of the reporting system. Results: A total of 115 HFs (including hospitals, health centres, and dispensaries) in 11 districts were assessed. Registers (availability rate=91.1%; interquartile range (IQR):66.7%-100%) and report forms (86.9%; IQR:62.2%-100%) were the most utilized HMIS tools. There was a limited use of tally-sheets (77.8%; IQR:35.6%-100%). Tools availability at the dispensary was 91.1%, health-centre 82.2% and hospital 77.8%, and was low in urban districts. The availability rate at the district level was 65% (IQR:48%-75%). Reports were highly over-represented in comparison to registers’ records, with large differences observed at the HF phase of the data journey and more profound in hospitals. Tool availability and data quality in the reproductive health service area outperformed the general services (outpatient and inpatient) areas. Indicators with large number of clients, multiple variables, disease categorization, or those linked with dispensing of medicine performed poorly. Conclusion: There are high variations in the tool utilisation and data accuracy at facility and district levels. A significant improvement on patient registration and use of tally-sheets was observed over the years. The routine HMIS is weak and data at district level inaccurately reflects what is available at the source (HFs). These results highlight the need to design tailored and inter-service strategies for improving data quality.