Free-standing archaeological walls are significantly exposed to horizontal actions (e.g., earthquakes) as they lack connections provided by floors or roofs. In such cases, the dynamic response governs the activation of local mechanisms of collapse, determining the shape of the macroblocks and their position. Engineering models of archaeological walls are developed according to the results of extensive visual inspections and on-site testing, including modal identification for calibration purposes. A modal response spectrum analysis on the calibrated model identifies the zones where the tensile stress is exceeded, which are more likely to detach as rigid macroblocks and subsequently overturn due to the expected ground spectra. The macroblocks are then assessed according to limit analysis. The case studies are the north and the apse walls of the church of San Giovanni Evangelista in Castelseprio (Varese, Lombardy), a 5th century Longobard fortified settlement, a part of UNESCO World Heritage. The construction quality of the apse was poorer than the north wall, but the masonry of both is very compact thanks to the good mortar. The macroblocks are identified mostly in the upper crests of the walls, and their acceleration of activation is two to six times larger than the demand (considering the dynamic amplification that the structure applies to the ground motion); therefore, no particular intervention is needed. The proposed method will require additional calibration, e.g., through nonlinear dynamic analyses, and a more precise treatment of uncertainties in masonry mechanical properties to determine the shape of the macroblocks.