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Abstract Background Implementation of the new Enhanced Primary Health Care (EnPHC) intervention aims to improve service quality and experience at primary healthcare clinics; especially to newly diagnosed patients. This was achieved by restructuring and improving existing services to better manage non-communicable diseases amongst patients. Objectives of this study are to explore patients’ experiences of the EnPHC intervention, to document their feedback and to determine effects of EnPHC intervention on patients. Methods This phenomenological qualitative study focussed on patients’ experiences in relation to EnPHC interventions. Participants were purposely selected from a group of patients who attended the eight intervention primary healthcare clinics in Johor and Selangor regularly for treatment. Data collection was conducted between April to July 2018. Semi-structured interviews were conducted at average an hour per interview for four to five patients per clinic. Interviews were audio recorded, transcribed verbatim, coded and analysed using a thematic analysis approach. Results A total of 35 patients participated. Analysis revealed five main themes about patient experiences receiving the EnPHC intervention. These are: (1) health assessment in disease progress monitoring, (2) patient-doctor relationship and continuity of care, (3) professionalism in service delivery, (4) ensuring compliance in achieving health targets and (5) communication skills. Each theme represents an important aspect of the service, how it should be delivered within the patient expectations and how it can improve patient’s health through their lens. Conclusion Even though patients were not able to exactly identify the EnPHC intervention components implemented, they are able to describe the process changes that occurred; enabling them to improve their healthcare status. Engagement is necessary to better inform patients of the EnPHC intervention, its purpose, mechanisms, changes and importance for healthcare. It would reduce resistance and increase awareness amongst patients at the clinic.