Micro-gas turbines are used for power generation and propulsion in unmanned aerial vehicles. Technological advancements to enhance their efficiency and fuel adaptability are continuously sought out. As part of a comprehensive study focused on understanding the fundamental performance and emission characteristics of a micro gas turbine model, with the aim of finding ways to enhance the operation of micro gas turbines, the current study uses a fully coupled whole-annulus simulation approach to systematically explore the combustor–turbine interaction without compromising the accuracy due to domain truncation. The numerical model is highly complex, spanning aerothermodynamics, fuel vaporization, combustion, and multi-species flow transport. Coupled with the realistic geometries of a representative micro-gas turbine, the proposed numerical model is highly accurate with the capability to capture the complex interaction between the flowfield and the aerothermodynamics and emission performances. The results show that unburnt gaseous Jet-A fuel is carried into the turbine domain through vortical flow structures originating from the combustion chamber. Notably, combustion processes persist within the turbine, leading to rapid Jet-A fuel concentration decay and linearly increasing soot concentration across the turbine domain. The relative circumferential positioning of the combustion chamber and turbine vane (i.e., clocking effects) profoundly influences micro-gas turbine aerothermodynamics and pollutant emissions. Leading-edge impingement hot-streak configurations enhance aerodynamic efficiency, while mid-passage hot-streak configurations mitigate aerothermal heat load and soot emissions. Clocking effects impact all parameters, indicating a complex interplay between the flowfield, aerothermal performance, and pollutant emissions. However, turbine vane heat load exhibits the most significant variations.