Diet-related chronic diseases are at epidemic levels in low-income ethnic minority populations. The purpose of this study is to decrease risk for obesity in children by modifying the food environment and conducting point-of-purchase promotions that will lead to changes in psychosocial factors and behaviors associated with healthier food choices among low-income communities with a preponderance of Native Hawaiians and Pacific Islanders. We implemented an intervention trial over a 9–11-month period in five food stores in two low-income multiethnic communities in Hawaii, targeting both children and their adult caregivers. The Healthy Foods Hawaii (HFH) intervention consisted of an environmental component to increase store stocking of nutritious foods, point-of-purchase promotions, interactive sessions, and involved local producers and distributors. We evaluated the impact of the program on 116 child–caregiver dyads, sampled from two intervention and two comparison areas before and after intervention implementation. Program impacts were evaluated using multivariable linear regression. The HFH program had a significant impact on caregiver knowledge and the perception that healthy foods are convenient. Intervention children significantly increased their Healthy Eating Index (HEI) score for servings of grains, their total consumption of water, and showed an average 8.5 point (out of 90 total, eliminating the 10 points for variety, giving a 9.4% increase) increase in overall HEI score. A food store intervention was effective in improving healthy food knowledge and perception that healthy foods are convenient among caregivers, and increased the consumption of several targeted healthy foods by their children. Greater intensity, sustained food system change, and further targeting for children are needed to show greater and sustained change in food-related behaviors in low-income Native Hawaiian and Pacific Islander communities.