The introduction of Universal Healthcare Coverage (JKN) in 2014 has changed the landscape of the Indonesian healthcare and affected the community pharmacy sector. This paper investigates perceptions of healthcare and pharmacy stakeholders about the impact of JKN on the practice of pharmacists and pharmacy in both public (Puskesmas) and private (Community or Retail pharmacy) settings. In‐depth, semi‐structured interviews were conducted from February to August 2016 involving 29 participants representing key stakeholders from different provinces in Indonesia. While JKN was actually designed with good policy objectives for pharmacy integration within primary care network, it has created some unintended and unanticipated distortion in the healthcare system which may be detrimental to the community pharmacy sector. In fact, community pharmacy practice is still limited to dispensing and continued to be hampered by ongoing challenges mainly pharmacists' absence, lack of clinical competence and limited support from regulation changes. It is a missed opportunity for pharmacists to play a greater role in primary care services indicating the need for an overhaul to pharmacy education and policy system.