This paper presents the results of palaeodietary reconstruction based on stable carbon and nitrogen isotope analysis on bone collagen of five medieval rural populations from the Basque Country (northern Spain) spanning from 5th to 15th centuries ad. One hundred forty‐seven human and 47 domestic faunal samples were successfully analysed with the objective of defining agrarian productive strategies and food consumption patterns. The results grouped the five sites in two clusters: on one side Zaballa and Treviño, whose inhabitants followed diets exclusively based on C3 plants with significant intake of animal protein, and on the other, the populations from Aistra and Zornoztegi, who combined C3 and C4 plants and consumed lower amounts of animal protein. The isotopic values from Dulantzi were intermediate to these two groups. No differences were detected when individual status markers, such as grave goods, were available. Conversely, some restrictions on the access to certain food resources based on sex were uncovered. A relevant change in δ13C values was identified around 10th century, a consequence of a shift in the consumption patterns of C3 and C4 plants. Finally, these Basque sites were compared with those of the medieval Iberian case studies available in the literature. This comparison made evident the distinctive nature of the diet of the Basque medieval rural contexts. Copyright © 2017 John Wiley & Sons, Ltd.