The aim of this paper is to introduce a model in which systematic effects can be assigned according to their origin or mode of action. The approach intends to improve the positional accuracy of a robot arm. We show the impact of unaccounted model biases on estimated parameters when applying sequential approaches and conclude the necessity of jointly determining all influencing variables. Therefore, we propose a simultaneous estimation of transformation parameters, robot’s kinematic parameters and non-geometric parameters modelled by an artificial neural network (ANN) in further consequence. Thus, the main contribution of this paper is a new approach of the simultaneous estimation of the geometric and non-geometric components of a robot arm model. The integration of the geometric model (transformations, kinematic robot model) with the non-geometric one (ANN) is realised in the extended Kalman filter. The functionality of the algorithm has been proven on simulated data. The adaptive behaviour of machine learning approaches is made possible by an additional iteration of the ANN. The initialisation of the ANN parameters must not deviate from the nominal parameters by more than 10% so that the ANN can learn the non-geometric part. In this setup, the robot arm position corrections are reduced by 32.5%. A final sensitivity analysis proves the estimability of most kinematic parameters in the course of a future adaptive extension of the approach.