Thermoelectric generators (TEGs) enable compact waste-heat energy harvesting but require high-gain DC–DC conversion due to their low output voltage for microgrid interfacing. This work proposes a novel TEG-supplied two-stage architecture consisting of a perturb and observe (P&O)-based MPPT boost converter followed by a modified Z-source converter regulated through an advanced control strategy. The modified Z-source topology enables high voltage gain without extreme duty ratios and mitigates switching losses by eliminating diode-related reverse-recovery effects via synchronous operation. To enhance dynamic performance, an advanced model predictive control (MPC) approach is adopted and benchmarked against conventional MPC and sliding mode control (SMC). Simulation results under hot-surface temperature variations demonstrate that the proposed system maintains stable 400-V DC bus regulation at a 100-W output level. In contrast, conventional MPC exhibits switching-frequency deviations that increase switching losses during transients, while conventional SMC suffers from significant voltage deviations. After the temperature variation tests, the proposed control strategy is subjected to a ±20% load test, in which it maintains 400-V regulation with nearly fixed-frequency operation, confirming its superior dynamic suitability for TEG-based systems operating at 50 kHz. The proposed innovative design provides a new perspective for TEG researchers while supporting sustainable waste-heat energy utilization.