The growing demand for healthy food products has created significant opportunities for businesses in the healthy food sector; however, maintaining customer loyalty remains challenging amid increasing competition and changing consumer preferences. In this context, understanding the mechanisms through which brand-related and store-related factors influence customer loyalty is essential for developing sustainable customer relationships. This study aims to examine the effects of brand image, perceived quality, and store atmosphere on customer loyalty through purchase decisions as a mediating variable at Healthy Food Grainsly Surabaya. The study employed a mixed-methods approach by integrating quantitative and qualitative data to obtain a comprehensive understanding of customer behavior. Quantitative data were collected from 100 respondents using an accidental sampling technique and analyzed using Structural Equation Modeling–Partial Least Squares (SEM-PLS). The findings reveal that brand image and store atmosphere do not have significant direct effects on customer loyalty. However, both variables demonstrate significant indirect effects on customer loyalty through purchase decisions, indicating that purchase decisions play an important mediating role in translating customer perceptions into loyalty. Meanwhile, perceived quality and purchase decisions have significant direct effects on customer loyalty. The structural model demonstrates strong explanatory and predictive capabilities, indicating that the selected variables provide meaningful explanations of customer loyalty behavior. These findings suggest that customer loyalty is shaped not only by favorable perceptions of a brand and retail environment but also by actual purchasing experiences and perceived product quality. Therefore, businesses should strengthen product quality, facilitate positive purchase decisions, and complement branding and store-atmosphere strategies to establish sustainable long-term customer loyalty.