Globally, diet is the leading risk for burden of disease. Diet is poorer and burden of disease higher for socio-economically disadvantaged populations in high and middle income countries. Strategies are urgently needed to address this inequity. We examined the effectiveness of a 20% price discount on selected purchases with and without nutrition education, delivered in store in remote Indigenous communities in Australia. A stepped-wedge randomised design was used, with 20 communities randomly assigned to 5 sets of 4 communities, spaced eight weeks apart. A 20% price discount on fresh and frozen fruit and vegetables, water and diet soft-drinks was applied for a period of 24 weeks in the community store. Two stores in each set were randomly assigned to receive a combined strategy (discount and education). Intervention effect was measured using mixed models employing weekly point-of-sale data for 131 weeks. The primary outcome was the percent change in fruit and vegetable purchases (grams) per person per day. The effect of applying the price discount was to increase sales of fruit and vegetables combined by 13% (4, 22), fruit 21% (7, 36), vegetables 9% (1,17), water 18% (1, 37), diet soft drink 5% (-6, 18), other foods 6% (-1, 13), regular soft drinks 6% (-3, 15) and other drinks 5% (-5, 15). The benefit of the in-store consumer nutrition education strategy was a further small increase in vegetable sales. Consistent with other studies, a price discount alone can shift food purchasing in low socio-economic communities.