Disclosed are fuel cell architectures, thermal sub-systems, and control logic for regulating fuel cell stack temperature. A method is disclosed for regulating the temperature of a fuel cell stack. The method includes determining a pre-start temperature of the fuel cell stack, and determining, for this pre-start temperature, a target heating rate to heat the stack to a calibrated minimum operating temperature. The method then determines a hydrogen bleed percentage for the target heating rate, and executes a stack heating operation including activating the fuel cell stack and commanding a fluid control device to direct hydrogen to the cathode side at the hydrogen bleed percentage to generate waste heat. After a calibrated period of time, the method determines if an operating temperature of the stack exceeds the calibrated minimum stack operating temperature. Responsive to the operating temperature being at or above the minimum operating temperature, the stack heating operation is terminated.