Introduction: Current intervention programme to improve drug adherence are either too complex or expensive for implementation and scale-up in low-middle-income countries. The aim of this study is to assess the process and effects of implementing a low-cost, targeted and tailored pharmacist intervention among patients with type 2 diabetes who are non-adherent to antihypertensive drugs in a real-world primary care Indonesian setting. Methods and analysis: A cluster randomised controlled trial with a 3-month follow-up will be conducted in 10 community health centres (CHCs) in Indonesia. Type 2 diabetes patients aged 18 years and older who reported non-adherence to antihypertensive drugs according to the Medication Adherence Report Scale (MARS) are eligible to participate. Patients in CHCs randomised to the intervention group will receive a tailored intervention based on their personal adherence barriers. Interventions may include reminders, habit-based strategies, family support, counselling to educate and motivate patients, and strategies to address other drug-related problems. Interventions will be provided at baseline and at a 1-month follow-up. Simple question-based flowcharts and an innovative adherence intervention wheel are provided to support the pharmacy staff. Patients in CHCs randomised to the control group will receive usual care based on the Indonesian guideline. The primary outcome is the between-group difference in medication adherence change from baseline to 3-month follow-up assessed by MARS. Secondary outcomes include changes in patients' blood pressure, their medication beliefs assessed by the Beliefs about Medicines Questionnaire (BMQ)-specific, as well as process characteristics of the intervention programme from a pharmacist and patient perspective. Ethics and dissemination: Ethical approval was obtained from the Ethical Committee of Universitas Padjadjaran, Indonesia (No. 859/UN6.KEP/EC/2019) and all patients will provide written informed consent prior to participation. The findings of the study will be disseminated through international conferences, one or more peer-reviewed journals and reports to key stakeholders.