Unreinforced masonry aggregate buildings represent a significant part of the architectural heritage in Mediterranean regions and continue to serve residential purposes despite their high vulnerability to seismic events, making their preservation critical. These structures have typically evolved through progressive expansions over time, forming heterogeneous compounds of interconnected units with varying geometries, materials, and slab typologies. This study proposes a numerical investigation of an elementary building aggregate building composed of three units. The finite element model of the aggregates is developed with the STKO software platform for OpenSees by adopting a homogenized approach using 2D layered shell elements to capture masonry walls’ complex behavior while maintaining reduced computational cost. Nonlinear dynamic analyses of the aggregate are carried out by varying the degree of connection between the units, the floor deformability and the height regularity. The results exhibit how the different units’ damage patterns and responses are affected by these variables evidencing the most and least critical conditions.