An application of an advanced anti-windup compensation scheme to a recently developed large-span track-seeking and track-following method for dual-stage actuator systems in hard disk drives (HDDs) is presented. In the original dual-stage servo control approach, micro-actuator saturation was addressed using the Circle Criterion to guide the controller design. However, such an approach does not allow the fine-tuning of seeking and settling speeds and also limits the class of linear controllers for the secondary loop due to the Circle Criterion. Anti-windup compensation removes many of these limitations and improves settling duration, disturbance rejection, recovery from saturation in the secondary actuator loop, and design flexibility. A general anti-windup (AW) compensator is presented in discrete time bringing together a number of AW concepts and results previously given in continuous time. Robustness is taken into account and performance requirements are expressed via frequency weights.