Randomised benchmarking is a widely used experimental technique to characterise the average error of quantum operations. Benchmarking procedures that scale to enable the characterisation of n-qubit circuits rely on efficient procedures for manipulating those circuits and, as such, have been limited to subgroups of the Clifford group. However, universal quantum computers require additional, non-Clifford gates to approximate arbitrary unitary transformations. We define a scalable randomised benchmarking procedure over n-qubit unitary matrices that correspond to protected non-Clifford gates for a class of stabiliser codes. We present efficient methods for representing and composing group elements, sampling them uniformly and synthesising corresponding poly (n)-sized circuits. The procedure provides experimental access to two independent parameters that together characterise the average gate fidelity of a group element.