We consider the $Sp(4)$ gauge theory coupled to $N_f=2$ fundamental and $n_f=3$ antisymmetric flavours of Dirac fermions in four dimensions. This theory serves as the microscopic origin for composite Higgs models with $SU(4)/Sp(4)$ coset, supplemented by partial top compositeness. We study numerically its lattice realisation, and couple the fundamental plaquette action to Wilson-Dirac fermions in mixed representations, by adopting a (rational) hybrid Monte Carlo method, to perform non-trivial tests of the properties of the resulting lattice theory. We find evidence of a surface (with boundaries) of first-order bulk phase transitions in the three-dimensional space of bare parameters (one coupling and two masses). Explicit evaluation of the Dirac eigenvalues confirms the expected patterns of global symmetry breaking. After investigating finite volume effects in the weak-coupling phase of the theory, for the largest available lattice we study the mass spectra of the lightest spin-0 and spin-1 flavoured mesons composed of fermions in each representation, and of the lightest half-integer spin composite particle made of fermions in different representations -- the chimera baryon. This work sets the stage for future systematical studies of the non-perturbative dynamics in phenomenologically relevant regions of parameter space.