The formation and evolution of stellar clusters is intimately linked to that of their host galaxies. To study this connection, we present the EMP-Pathfinder suite of cosmological zoom-in Milky Way-mass simulations. These simulations contain a sub-grid description for stellar cluster formation and evolution, allowing us to study the simultaneous formation and evolution of stellar clusters alongside their host galaxies across cosmic time. As a key ingredient in these simulations, we include the physics of the multi-phase nature of the interstellar medium (ISM), which enables studies of how the presence of a cold, dense ISM affects cluster formation and evolution. We consider two different star formation prescriptions: a constant star formation efficiency per free-fall time, as well as an environmentally-dependent, turbulence-based prescription. We identify two key results drawn from these simulations. Firstly, we find that tidal shock-driven disruption caused by the graininess of the cold ISM produces old (𝜏 > 10 Gyr) stellar cluster populations with properties that are in excellent agreement with the observed populations in the Milky Way and M31. Importantly, the addition of the cold ISM addresses the areas of disagreement found in previous simulations that lacked the cold gas phase. Secondly, the formation of stellar clusters is extremely sensitive to the baryonic physics that govern the properties of the cold, dense gas reservoir in the galaxy. This implies that the demographics of stellar cluster populations represent an important diagnostic tool for constraining baryonic physics models in upcoming galaxy formation simulations that also include a description of the cold ISM.