The authors investigate a disturbance-compensating and energy-saving control method for air turbine spindles equipped with a rotation control system designed for use in ultra-precision milling. The controllability and energy-conserving characteristics of the proposed method using the proposed pneumatic regulating device, called a high-precision quick-response pneumatic pressure regulator, were demonstrated experimentally previously. Herein, the proposed rotation-controlled air turbine spindle is first summarised. Subsequently, the proposed rotation-controlled air turbine spindle is set to a milling machine and applied to the milling of an alloy tool steel, to gain data and validate the effectiveness of the in-process tool wear estimation method that have been recently developed and proposed by the authors. Particularly, to evaluate the possibility of applying the proposed estimation method to three-dimensional milling, milling experiments where the air turbine spindle is set at a 45° incline were conducted and the results indicate a high possibility of the proposed method.