We apply pseudo-spectral methods to integrate functional flow equations with high accuracy, extending earlier work on functional fixed point equations [1]. The advantages of our method are illustrated with the help of two classes of models: first, to make contact with literature, we investigate flows of the O(N )-model in 3 dimensions, for N = 1, 4 and in the large N limit. For the case of a fractal dimension, d = 2.4, and N = 1, we follow the flow along a separatrix from a multicritical fixed point to the Wilson-Fisher fixed point over almost 13 orders of magnitude. As a second example, we consider flows of bounded quantum-mechanical potentials, which can be considered as a toy model for Higgs inflation. Such flows pose substantial numerical difficulties, and represent a perfect test bed to exemplify the power of pseudo-spectral methods.