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Summary: This paper reports an immersion and invariance (I&I)–based robust nonlinear controller for atomic force microscope (AFM) applications. The AFM dynamics is prone to chaos, which, in practice, leads to performance degradation and inaccurate measurements. Therefore, we design a nonlinear tracking controller that stabilizes the AFM dynamics around a desired periodic orbit. To this end, in the tracking error state space, we define a target invariant manifold, on which the system dynamics fulfills the control objective. First, considering a nominal case with full state measurement and no modeling uncertainty, we design an I&I controller to render the target manifold exponentially attractive. Next, we consider an uncertain AFM dynamics, in which only the displacement of the probe cantilever is measured. In the framework of the I&I method, we recast the robust output feedback control problem as the immersion of the output feedback closed‐loop system into the nominal full state one. For this purpose, we define another target invariant manifold that recovers the performance of the nominal control system. Moreover, to handle large uncertainty/disturbances, we incorporate the method of active disturbance rejection into the I&I output feedback control. Through Lyapunov‐based analysis of the closed‐loop stability and robustness, we show the semiglobal practical stability and convergence of the tracking error dynamics. Finally, we present a set of detailed, comparative software simulations to assess the effectiveness of the control method. [ABSTRACT FROM AUTHOR]