In this paper, we propose a mesh-free numerical method for solving elliptic PDEs on unknown manifolds, identified with randomly sampled point cloud data. The PDE solver is formulated as a spectral method where the test function space is the span of the leading eigenfunctions of the Laplacian operator, which are approximated from the point cloud data. While the framework is flexible for any test functional space, we will consider the eigensolutions of a weighted Laplacian obtained from a symmetric Radial Basis Function (RBF) method induced by a weak approximation of a weighted Laplacian on an appropriate Hilbert space. In this paper, we consider a test function space that encodes the geometry of the data yet does not require us to identify and use the sampling density of the point cloud. To attain a more accurate approximation of the expansion coefficients, we adopt a second-order tangent space estimation method to improve the RBF interpolation accuracy in estimating the tangential derivatives. This spectral framework allows us to efficiently solve the PDE many times subjected to different parameters, which reduces the computational cost in the related inverse problem applications. In a well-posed elliptic PDE setting with randomly sampled point cloud data, we provide a theoretical analysis to demonstrate the convergence of the proposed solver as the sample size increases. We also report some numerical studies that show the convergence of the spectral solver on simple manifolds and unknown, rough surfaces. Our numerical results suggest that the proposed method is more accurate than a graph Laplacian-based solver on smooth manifolds. On rough manifolds, these two approaches are comparable. Due to the flexibility of the framework, we empirically found improved accuracies in both smoothed and unsmoothed Stanford bunny domains by blending the graph Laplacian eigensolutions and RBF interpolator. •Solving elliptic PDEs on manifolds identified with random point cloud data.•An efficient PDE solver based on Galerkin framework.•Approximate eigenfunctions on manifold using Radial Basis Function approximation.