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Quantum systems are typically subject to various environmental noise sources. Treating these environmental disturbances with a system-bath approach beyond weak coupling, one must refer to numerical methods as, for example, the numerically exact quasi-adiabatic path integral approach. This approach, however, cannot treat baths which couple to the system via operators, which do not commute. We extend the quasi-adiabatic path integral approach by determining the time discrete influence functional for such non-commuting fluctuations and by modifying the propagation scheme accordingly. We test the extended quasi-adiabatic path integral approach by determining the time evolution of a quantum two-level system coupled to two independent baths via non-commuting operators. We show that the convergent results can be obtained and agreement with the analytical weak coupling results is achieved in the respective limits.