Inadequate consumption of healthy food is an ongoing public health issue in the United States. Food availability measures of supply versus consumption of healthy foods are disconnected in many studies. There is a need for an objective assessment of the food environment in order to assess how the food supply aligns with the Healthy Eating Index (HEI). Data were collected as part of the Healthy Community Stores Case Study Project, including a refined Nutrition Environment Measures Survey for Healthy Community Stores (NEMS-HCS) and an updated Healthy Food Availability Index that aligns with the Healthy Eating Index (HFAHEI). This paper will focus on the NEMS-HCS development process, findings, and HFAHEI application. All food items were more likely to be found at grocery stores rather than corner stores. Food pricing was often above the Consumer Price Index averages for six food items. The NEMS-HCS assessment better aligned with the HEI because it included a wider variety of meats, frozen fruits and vegetables, and an increased selection of whole grains. HFAHEI scoring was inclusive of non-traditional and alternative community stores with a health focus, making it suitable for use at the local level, especially in neighborhoods where supermarkets and large chain stores are less common.