The seismic capacity of buildings is usually studied through separate analysis of two orthogonal directions, then combined using empirical rules. Nevertheless, the three-dimensional nature of seismic action gives rise to interaction among its different components, especially the two horizontal ones, which can cause substantial discrepancy between the actual 3D response and the one obtained by combining uniaxial responses. The present study addresses this problem for waffle-flat-plate (WFP) structures with an irregular layout of columns from the standpoint of energy dissipation capacity. A portion of a WFP prototype structure that was built in Laboratory was subjected, simultaneously, to two horizontal components of a far-field seismic record upon a shake-table. Several shakings of increasing intensity were applied until the collapse of the structure. Afterwards, a numerical model of the specimen was developed and validated with the experimental results. The numerical model was subjected to several sets of ground motions having diverse ratios of energy input from the horizontal components. When the total energy dissipated by the structure through cumulative plastic deformations until failure was obtained for each set of accelerograms, a fairly stable quantity was found to be concentrated within a narrow range of values. Moreover, the specimen subjected to bi-directional seismic loading showed a higher ultimate energy dissipation capacity than under uni-directional loadings.