OBJECTIVE Little is known about the practices for stocking and procuring healthy food in non-traditional food retailers (e.g., gas-marts, pharmacies). The present study aimed to: (i) compare availability of healthy food items across small food store types; and (ii) examine owner/manager perceptions and stocking practices for healthy food across store types. METHODS Descriptive analyses were conducted among corner/small grocery stores, gas-marts, pharmacies and dollar stores. Data from store inventories were used to examine availability of twelve healthy food types and an overall healthy food supply score. Interviews with managers assessed stocking practices and profitability. METHODS Small stores in Minneapolis and St. Paul, MN, USA, not participating in the Special Supplemental Nutrition Program for Women, Infants, and Children. METHODS One hundred and nineteen small food retailers and seventy-one store managers. RESULTS Availability of specific items varied across store type. Only corner/small grocery stores commonly sold fresh vegetables (63% v. 8% of gas-marts, 0% of dollar stores and 23% of pharmacies). More than half of managers stocking produce relied on cash-and-carry practices to stock fresh fruit (53%) and vegetables (55%), instead of direct store delivery. Most healthy foods were perceived by managers to have at least average profitability. CONCLUSIONS Interventions to improve healthy food offerings in small stores should consider the diverse environments, stocking practices and supply mechanisms of small stores, particularly non-traditional food retailers. Improvements may require technical support, customer engagement and innovative distribution practices.