With a model-based control strategy, the effectiveness of the associated control action depends on the availability of a <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">representative</i> control-oriented model. In the case of floating offshore wave energy converters (WECs), the device response depends upon the interaction between mooring system, any mechanical parts, and the hydrodynamics of the floating body. This study proposes an approach to synthesise WEC controllers under the effect of mooring forces building a representative data-based linear model able to include any relevant dynamics. Moreover, the procedure is tested on the moored pendulum wave energy converter (PeWEC) by means of a high-fidelity mooring solver, OrcaFlex (OF). In particular, the control action is computed with and without knowledge of the mooring influence, in order to analyse and elucidate the effect of the station-keeping system on the harvested energy. The performance assessment of the device is achieved by evaluating device power on the resource scatter characterising Pantelleria, Italy. The results show the relevance of the mooring dynamics on the device response and final set of control parameters and, hence, a significant influence of the station-keeping system on control synthesis and extracted mechanical power.