A method is presented for tooltip tracking in active magnetic bearing (AMB) spindle applications. The proposed tool tracking approach uses control of the AMB air gap to achieve the desired tool position. A μ-synthesis-based controller is designed for the AMBs with the goal of robustly minimizing the difference between the tool reference and estimated tool position. In such a way, the model-based control approach concurrently addresses the tracking problem and the inability to directly measure real-time tool position in the presence of machining disturbances. To ensure the tractability of the control problem, a model of the desired tracking dynamics is included in the plant. The method is demonstrated on a high-speed AMB boring spindle. To confirm the tool tracking capability, characteristic part geometries are traced including stepped, tapered, and convex profiles. Tool tracking is demonstrated for the rotating AMB spindle in the range of 90 μm. Also, static and dynamic external loading is applied to the spindle tool location to confirm the disturbance rejection ability of the closed-loop system.