We present an optimization-based reference trajectory tracking method for quadrotor robots for slow-speed maneuvers. The proposed method uses planning followed by the controlling paradigm. The basic concept of the proposed method is an analogy to Linear Quadratic Gaussian (LQG) in which Nonlinear Model Predictive Control (NMPC) is employed for predicting optimal control policy in each iteration. Multiple-shooting (MS) is suggested over Direct-collocation (DC) for imposing constraints when modelling the NMPC. Incremental Euclidean Distance Transformation Map (EDTM) is constructed for obtaining the closest free distances relative to the predicted trajectory; these distances are considered obstacle constraints. The reference trajectory is generated, ensuring dynamic feasibility. The objective is to minimize the error between the quadrotor’s current pose and the desired reference trajectory pose in each iteration. Finally, we evaluated the proposed method with two other approaches and showed that our proposal is better than those two in terms of reaching the goal without any collision. Additionally, we published a new dataset, which can be used for evaluating the performance of trajectory tracking algorithms.