An adaptive capacity constraint management system receives a measured value affected by HVAC equipment at actual operating conditions and uses the measured value to determine an operating value for a variable that affects a capacity of the HVAC equipment at the actual operating condition. The system uses the operating value to calculate a gain factor for the variable relative to design conditions and uses the calculated gain factor to determine a capacity gain for the HVAC equipment relative to the design conditions. The system applies the capacity gain to a design capacity limit for the HVAC equipment to determine a new capacity limit for the HVAC equipment at the actual operating conditions. The system may use the new capacity limit as a constraint in an optimization routine that that selects one or more devices of the HVAC equipment to satisfy a load setpoint.