Methods and apparatus for controlling manufacturing equipment are provided herein. In some embodiments, a manufacturing system may include an integrated controller having one or more inputs to receive input values corresponding to operating information of at least one of a process tool, a mass flow controller or at least one sub-fab auxiliary system, wherein the integrated controller is configured to receive the input values, determine that an error condition is matched based on the received input values, and control the at least one sub-fab auxiliary system to operate at a fail-safe operating mode responsive to the determined error condition.