A novel approach for robust controller synthesis, which models uncertainty as an elliptical set, is proposed in the paper. Given a set of frequency response functions of linear time-invariant (LTI) multiple-input multiple-output (MIMO) systems, the approach determines the ‘best’ linear nominal model and the corresponding elliptical uncertainty set, which is consistent with the data. Using a novel split representation, the uncertainty set is represented as an equivalent integral quadratic constraint (IQC). Finally, this IQC is integrated into a data-driven frequency-domain controller synthesis method using convex optimisation. The proposed method is used to design a controller, which is robust against mechanical un- certainties for a hybrid micro-disturbance isolation platform for space applications. The experimental results show that the proposed method provides a less conservative uncertainty set and improves attenuation performance compared to classical methods that use disk uncertainty.