In recent years, sparse spectral methods for solving partial differential equations have been derived using hierarchies of classical orthogonal polynomials on intervals, disks, disk-slices and triangles. In this work we extend the methodology to a hierarchy of non-classical multivariate orthogonal polynomials on spherical caps. The entries of discretisations of partial differential operators can be effectively computed using formulae in terms of (non-classical) univariate orthogonal polynomials. We demonstrate the results on partial differential equations involving the spherical Laplacian and biharmonic operators, showing spectral convergence.