A method of operating a reactor system to provide multi-zone substrate temperature control. The method includes, with a first pyrometer, sensing a temperature of a first zone of a substrate supported in the reactor system, and, with a second pyrometer, sensing a temperature of a second zone of the substrate. The method further includes, with a controller, comparing the temperatures of the first and second zones to setpoint temperatures for the first and second zones and, in response, generating control signals to control heating of the substrate. The method also includes controlling, based on the control signals, operations of a heater assembly operating to heat the substrate.