Background: The Republic of Moldova is faced with a high prevalence of non-communicable diseases (NCDs) related to lifestyle and health behavioural factors. Within the frame of the decentralisation reform, the primary health care system has been tasked to play an important role in the provision of preventative and curative NCD health services. There is however limited evidence available on the actual coverage and quality of care provided. Our paper aims to provide an updated overview of the coverage and quality of service provision in rural and urban regions of Moldova. Methods: We designed a facility-based survey to measure aspects of coverage and quality of care of NCD services across 20 districts of the Republic of Moldova. This study presents descriptive data on the structural, procedural and clinical aspects of primary healthcare delivery at health centre and family doctor office level. Adjacent private pharmacies were also assessed for the availability of essential NCD medicine. Results: Organised under the WHO Health Systems Framework, our findings highlight that service provision and information were generally the strongest among the six health systems building blocks, with more weaknesses found in the area of the health workforce, medical products, financing, and leadership/governance. Urban facilities generally fared better across all indicators. Conclusions: The gaps in service provision identified by this study require broad health system improvements to ensure NCD related policies and strategies are embedded in primary health care service provision. This likely calls for stronger coordination and collaboration between the public and private sectors and the different levels of government working towards ensuring universal health coverage in Moldova.