Abstract In this work, we present a Flux-Corrected Transport (FCT) algorithm for enforcing discrete maximum principles in Radial Basis Function (RBF) generalized Finite Difference (FD) methods for convection-dominated problems. The algorithm is constructed to guarantee mass conservation and to preserve positivity of the solution for irregular data nodes. The method can be applied both for problems defined in a domain or if equipped with level set techniques, on a stationary manifold. We demonstrate the numerical behavior of the method by performing numerical tests for the solid-body rotation benchmark in a unit square and for a transport problem along a curve implicitly prescribed by a level set function. Extension of the proposed method to higher dimensions is straightforward and easily realizable.