The growing demand for healthy food products has intensified competition among businesses, making customer loyalty an important determinant of sustainable business performance. This study aims to examine the effects of brand image, perceived quality, and store atmosphere on customer loyalty through purchase decision as a mediating variable at Grainsly Surabaya, Indonesia. The study employed a mixed-methods approach by integrating quantitative and qualitative data to obtain a comprehensive understanding of customer behavior. Data were collected from 100 respondents selected using an accidental sampling technique and analyzed using Structural Equation Modeling–Partial Least Squares (SEM-PLS). The results indicate that brand image and store atmosphere do not have significant direct effects on customer loyalty. However, both variables have significant indirect effects on customer loyalty through purchase decision, indicating that purchase decision plays an important mediating role. In contrast, perceived quality and purchase decision have significant direct effects on customer loyalty. The findings further demonstrate that the proposed model has strong explanatory and predictive relevance in explaining customer loyalty behavior. These results suggest that customer loyalty is shaped not only by customers’ perceptions of a brand and retail environment but also by their actual purchase decisions and perceptions of product quality. Therefore, Grainsly should strengthen product quality, facilitate positive purchase experiences, and integrate branding and store atmosphere strategies to encourage purchase decisions and foster sustainable customer loyalty.