The remains of the archaeological site of Castelseprio (Varese province, Italy) are listed under the UNESCO World Heritage as proof of one of the seven settlements of the Lombards in Italy. Freestanding elements belonging to the apse and the lateral walls of the church of San Giovanni Evangelista are still preserved nowadays, reaching heights around 5 and 10 m, respectively. The condition of these walls, both in terms of slenderness and incompleteness, constitutes a possible vulnerability under horizontal actions that would need to be assessed for conservation. In particular, the presence of multi-leaf and/or low-compact sections could limit the structural capacity of the walls and contribute to brittle collapses, even under low forces. According to the analyses of mortars carried out in the excavation site, the specific characteristics of the local geo-resources (clay-rich sediments traditionally called “Ferretto” deposits) directly influenced the incidence of pozzolanic binding processes, allowing the formation of two different aluminosilicate-based reaction products based on a standard calcic system (C-A-S-H) and on a magnesian one (M-A-S-H). This peculiar reuse of local lateritic soils, with a high concentration in the bedding mortars of the foundational structures, increased not only the general durability of the masonry but also the mechanical properties of the first architectural complex of San Giovanni. Based on the types of mortar identified, various configurations of wall sections were assumed (monolithic and multi-layered) and their mechanical behaviour through kinematic analyses was compared, to evaluate the relevant limits of the seismic capacity of the walls.