To maximize the potential for high material removal rates in simultaneous processes such as parallel milling, developing strategies for successful chatter suppression/avoidance is an important concern for manufacturers. In this study, the effectiveness of the spindle speed difference method (SDM) for chatter suppression is discussed in a parallel end-milling process where a flexible workpiece is machined by two tools rotating in opposite direction. The process model is developed, considering that the dynamic variation due to the regenerative effect occurs on a plane perpendicular to the tool axis direction. Through the process simulations and the experiments, this study provides informative discussion for comprehending the process behavior. Additionally, a real-time active chatter suppression system with adaptive SDM, where the spindle speed difference is sequentially optimized during the process according to the tracked chatter frequency, is developed by integrating a chatter monitoring system based on sensorless cutting force estimation with sliding discrete Fourier transform. The results show that the developed real-time adaptive system of spindle speed suppresses chatter vibrations more effectively than non-adaptive SDM system; hence, the integrated system can contribute self-optimizing machining systems oriented to Industry 4.0. Keywords Parallel milling • Chatter • Process control • Speed difference method • Disturbance observer Abbreviations a p Axial depth of cut a t Acceleration of table c f Feed per tooth dF t , dF r , dF a Minute cutting force in tool tangential, radial, and axial directions dF x , dF y , dF z Minute cutting force in Cartesian coordinate system F cut Cutting force F stat Non-process-related force including friction and gravity terms F x , F y , F z Cutting force in Cartesian coordinate system g(θ) Unit step function to judge tooth engagement G(iω) Frequency response function G LPF (s) Low-pass filter h Uncut chip thickness I a ref Motor current reference J r Total inertia of motor, coupling, and ball screw k c Chatter lobe number K t Torque coefficient K te , K re , K ae Edge force coefficient in tangential, radial, and axial directions K tc , K rc , K ac Cutting force coefficients in tangential, radial, and axial directions