In this paper, we carry out a systematic comparison between the theoretical properties of Spectral Element Methods and NURBS-based Isogeometric Analysis in its basic form, that is in the framework of the Galerkin method, for the approximation of the Poisson problem, which we select as a benchmark Partial Differential Equation. Our focus is on their convergence properties, the algebraic structure and the spectral properties of the corresponding discrete arrays (mass and stiffness matrices). We review the available theoretical results for these methods and verify them numerically by performing an error analysis on the solution of the Poisson problem. Where theory is lacking, we use numerical investigation of the results to draw conjectures on the behaviour of the corresponding theoretical laws in terms of the design parameters, such as the (mesh) element size, the local polynomial degree, the smoothness of the NURBS basis functions, the space dimension, and the total number of degrees of freedom involved in the computations.