As technology evolves, more complex non-affine systems are created. These complex systems are hard to model, whereas most controllers require information on systems to be designed. This information is hard to obtain for systems with varying control directions. Therefore, this study introduces a novel data-driven estimator and controller tailored for single-input single-output non-affine discrete-time systems. This approach focuses on cases when the control direction varies over time and the mathematical model of the system is completely unknown. The estimator and controller are constructed using a Multiple-input Fuzzy Rules Emulated Network framework. The weight vectors are updated through the gradient descent optimization method, which employs a unique cost function that multiplies the error by a hyperbolic tangent. The stability analyses demonstrate that both the estimator and controller converge to uniformly ultimately bounded (UUB) functions of Lyapunov. To validate the results, we show experimental tests of force control that were executed on the z-axis of a drive-controlled 3D scanning robot. This system has a varying control direction, and we also provide comparison results with a state-of-the-art controller. The results show a mean absolute percentage tracking error smaller than one percent on the steady state and the expected variation in the system’s control direction.