The Iberian Peninsula was at the forefront of the religious, economic, and political changes that swept across Europe during the Medieval Period, including the expansion of Christianity following the disintegration of the Umayyad Caliphate. Between the 9th and the 13th centuries CE, northern Iberia, in particular, witnessed a marked demographic and economic expansion that accompanied the emergence and development of different Christian Kingdoms. A growth in religious infrastructure driven by territorial expansion at the expense of Al-Andalus, and the emerging importance of the Camino de Santiago (the Way of St. James) from the 11th century CE, represented vital processes in changing urban networks and social stratification. However, shifting diets and social structures brought about by these changes require direct study beyond historical texts or localised osteoarchaeological and biomolecular studies in order to determine their wider impacts on peoples’ lived experience. Here, we apply radiocarbon dating (n = 6) and stable carbon and nitrogen isotope analysis to bone and dentine collagen from various locations (n = 10) across the north and north-eastern areas of modern Spain, where three prominent Medieval Christian Kingdoms (Aragon, Castille and Navarre) developed. We sampled 40 human and 32 faunal remains dating to between the 9th and 13th centuries CE, including historical personages such as Sancho Ramirez, Count of Ribagorza and an illegitimate son of King Ramiro I of Aragon; Saint Raymond William or San Ramón de Roda; Pedro de Librana, the first bishop of the city of Zaragoza after its conquest by the Christians in the 12th century CE; an unknown princess from the royal house of Aragon; and individuals from the urban and rural nuclei of Pamplona, Logroño, Lobera de Onsella (Zaragoza), and San Roque de las Quintanillas (Burgos). We compared our results to existing data from the same area demonstrating clear differences in access to animal protein and marine/freshwater resources between rural, urban, and high social status populations on a regional scale. Our data show significant differences in δ15N values between the different groups, with the highest values seen among the ‘elite’, followed by urban populations who benefited from trade and socio-economic diversity. This dataset acts as an important reference point for future studies focusing on changes in the diet and health among different sectors of Medieval society and, in particular, the development of social inequality in the Christian Kingdoms of Iberia as they formed at the centre of novel cultural and religious exchanges across Europe.