The structural performance of critical infrastructure during extreme events requires testing to understand the complex dynamics. Shake table testing of buildings to evaluate structural integrity is expensive and requires special facilities that can allow for the construction of large-scale test specimens. An attractive alternative is a cyber-physical testing technique known as Real-Time Hybrid Simulation (RTHS), where a large-scale structure is decomposed into physical and numerical substructures. A transfer system creates the interface between physical and numerical substructures. The challenge occurs when using multiple actuators connected with a coupler (i.e., transfer system) to create translation and rotation at the interface. Tracking control strategies aim to reduce time delay errors to create the desired displacements that account for the complex dynamics. This paper proposes two adaptive control methodologies for multi-axial real-time hybrid simulations that improve capabilities for a higher degree of coupling, boundary, complexity, and noise reduction. One control method integrates the feedback proportional derivative integrator (PID) control with a conditional adaptive time series (CATS) compensation and inverse decoupler. The second proposed control method is based on a coupled Model Predictive Control (MPC) with the CATS compensation. The performance of the proposed methods is evaluated using the virtual multi-axial benchmark control problem consisting of a steel frame as the experimental substructure. The transfer system consists of a coupler that connects two hydraulic actuators generating the translation and rotation acting at the joint. Through sensitivity analysis, parameters were tuned for the decoupler components, CATS compensation, and the control design for PID, LQG, and MPC. Comparative results among different control methods are evaluated based on performance criteria, including critical factors such as reduction in the time delay of bothactuators. The research findings in this paper improve the tracking control systems for the multi-axial RTHS of building structures subjected to earthquake loading. It provides insight into the robustness of the proposed tracking control methods in addressing uncertainty and improves the understanding of multiple output controllers that could be used in future cyber-physical testing of civil infrastructure subjected to natural hazards.