Improving healthy food access in low-income communities continues to be a public health challenge. One strategy for improving healthy food access has been to introduce community food stores, with the mission of increasing healthy food access; however, no study has explored the experiences of different initiatives and models in opening and sustaining healthy food stores. This study used a case study approach to understand the experiences of healthy food stores in low-income communities. The purpose of this paper is to describe the methodology used and protocol followed. A case study approach was used to describe seven healthy food stores across urban settings in the U.S. Each site individually coded their cases, and meetings were held to discuss emerging and cross-cutting themes. A cross-case analysis approach was used to produce a series of papers detailing the results of each theme. Most case studies were on for-profit, full-service grocery stores, with store sizes ranging from 900 to 65,000 square feet. Healthy Food Availability scores across sites ranged from 11.6 (low) to 26.5 (high). The papers resulting from this study will detail the key findings of the case studies and will focus on the challenges, strategies, and experiences of retail food stores attempting to improve healthy food access for disadvantaged communities. The work presented in this special issue will help to advance research in the area of community food stores, and the recommendations can be used by aspiring, new, and current community food store owners.