A direct output feedback control scheme was recently proposed by the authors for single-story building structures resting on flexible soil body. In this paper, the control scheme is extended to mitigate the seismic responses of multi-story buildings. Soil-structure interaction is taken into account in two parts: input at the soil-structure interface/foundation and control algorithm. The former reflects the effect on ground motions and is monitored in real time with accelerometers at foundation. The latter includes the effect on the dynamic characteristics of structures, which is formulated by modifying the classical linear quadratic regulator based on the fundamental mode shape of the soil-structure system. Numerical result on the study of a $frac{1}{4}$-scale three-story structure, supported by a viscoelastic half-space of soil mass, have demonstrated that the proposed algorithm is robust and very effective in suppressing the earthquake-induced vibration in building structures even supported on a flexible soil mass. Parametric studies are performed to understand how soil damping and flexibility affect the effectiveness of active tendon control. The selection of weighting matrix and effect of soil property uncertainty are investigated in detail for practical applications.