Introduction Nearly 90% of all deaths in the Republic of Moldova are caused by non-communicable diseases, the majority of which (55%) are caused by cardiovascular diseases (CVD). In addition to reducing premature mortality from CVD, it is estimated that strengthening primary healthcare could cut the number of hypertension-related hospital admissions and diabetes-related hospitalisations in half. The aim of this evaluation is to determine the feasibility of implementing and evaluating essential interventions for the prevention of CVD in primary healthcare in the Republic of Moldova, with a view towards national scale-up. Methods and analysis A national steering group including international experts will be convened to adapt WHO Package of Essential NCD Intervention from Primary Healthcare in Low Resource Settings protocols 1 and 2 to the health system of the Republic of Moldova, develop and conduct training of primary healthcare workers and test a core set of indicators to monitor the quality of care and change in clinical practice. To evaluate the impact of this pilot implementation, a pragmatic, sequential mixed methods explanatory design, composed of quantitative and qualitative strands of equal weight, will be used. Twenty primary healthcare centres will be selected and randomised to the training and implementation arm (n=10) and the usual care arm (n=10). At baseline and 12 months follow-up, a standardised data collection form will be piloted to extract data directly from patient paper records in order to estimate the change in clinical practice. Semi-structured interviews and interclinic peer workshops will be conducted at 12 months follow-up, and qualitative data collected from these formats will be analysed thematically for explanatory themes that relate to the quantitative findings. Ethics and dissemination Ethical review and approval has been obtained. Findings of the evaluation will be shared in a project report to key stakeholders, presented back to participants and written into a manuscript for an open access peer-reviewed scientific journal.