Background Successful implementation and long-term maintenance of healthy supermarkets initiatives are crucial to achieving potential population health benefits. Understanding barriers and enablers of implementation of real-world trials will enhance wide-scale implementation. This process evaluation of a healthy supermarket intervention sought to describe (i) customer, retailer and stakeholder perspectives on the intervention; (ii) intervention implementation; and (iii) implementation barriers and enablers. Methods Eat Well @ IGA was a 12-month randomised controlled trial conducted in 11 Independent Grocers of Australia (IGA) chain supermarkets in regional Victoria, Australia (5 intervention and 6 wait-listed control stores). Intervention components included trolley and basket signage, local area and in-store promotion, and shelf tags highlighting the healthiest packaged foods. A sequential mixed-methods process evaluation was undertaken. Customer exit surveys investigated demographics, and intervention recall and perceptions. Logistic mixed-models estimated associations between customer responses and demographics, with store as random effect. Supermarket staff surveys investigated staff demographics, interactions with customers, and intervention component feedback. Semi-structured stakeholder interviews with local government, retail and academic partners explored intervention perceptions, and factors which enabled or inhibited implementation, maintenance and scalability. Interviews were inductively coded to identify key themes. Results Of 500 customers surveyed, 33%[95%CI:23,44] recalled the Eat Well @ IGA brand and 97%[95%CI:93,99] agreed that IGA should continue its efforts to encourage healthy eating. The 82 staff surveyed demonstrated very favourable intervention perceptions. Themes from 19 interviews included that business models favour sales of unhealthy foods, and that stakeholder collaboration was crucial to intervention design and implementation. Staff surveys and interviews highlighted the need to minimise staff time for project maintenance and to regularly refresh intervention materials to increase and maintain salience among customers. Conclusions This process evaluation found that interventions to promote healthy diets in supermarkets can be perceived as beneficial by retailers, customers, and government partners provided that barriers including staff time and intervention salience are addressed. Collaborative partnerships in intervention design and implementation, including retailers, governments, and academics, show potential for encouraging long-term sustainability of interventions.