This article discusses the application and implications of magnetic prospection within two complex early mediaeval sites of the 5th–10th centuries BCE in northern Spain, at Aistra and Peña Amaya in the Upper Ebro Valley. In this period most sites displaying domestic and other forms of occupation present multifaceted and challenging problems due to the poor preservation of stratigraphic relationships in rural contexts and rarity and poor visibility of early mediaeval horizons in multi‐period urban sites. It is now widely acknowledged that extensive magnetic prospection, both in rural areas and in abandoned townscapes, can on a variety of sites facilitate the identification of domestic settlements, productive areas and monumental structures as well as the patterns of former roads, trackways and field boundaries. The two sites described here were selected to test this approach in the particular environment of the Ebro Valley and to draw any resulting conclusions about early mediaeval settlement in the area.