Lately, economies have been facing an increase in the frequency and magnitude of droughts, which come with potential consequences on food prices. This article aims to analyze how drought disturbances affect price differences in local food markets. Special attention is paid to differences in product quality and marketing channels. To study the mechanism behind price differences, our analysis is framed within the food market integration theory. Our methodology follows a dyadic regression approach, which allows us to exploit the panel data structure of our market price data. We use monthly Asterix potato and long shelf-life tomato market prices from traditional markets and supermarkets in Chile. To measure drought intensity, we use remote sensing data to construct a drought index. Results show that drought shocks reduce market price differentials around harvesting and commercialization periods, which is supported by the existence of market integration. We also find that prices of high-quality products, less perishable products, and those taken from traditional markets respond more intensively to droughts and take more time to be transmitted. A direct link between droughts and crop quality, as well as supermarkets’ larger capacity for buffer stock, may be behind these interpretations. Product differentiation and retail price rigidity arguments are also discussed.