We present a low-depth randomised algorithm for the estimation of entanglement fidelity between an n-qubit matchgate circuit U and its noisy implementation E. Our procedure makes use of a modified Pauli-Liouville representation of quantum channels, with Clifford algebra elements as a basis. We show that this choice of representation leads to a block-diagonal compound matrix structure of matchgate superoperators which enables construction of efficient protocols for estimating the fidelity, achieving a 1/n speedup over protocols of Flammia & Liu [PRL 106, 230501]. Finally, we offer simple extensions of our protocol which (without additional overhead) benchmark matchgate circuits intertwined by Clifford circuits, and circuits composed of exclusively nearest-neighbour XY(θ) gates or Givens rotations - forming the first known method for direct benchmarking of matchgate subgroups.