Solid-state nanopores of only a few nanometres in size show a great potential for applications such as molecule detection and DNA sequencing. In most cases, the fabrication of such a nanopore requires the high energy beam of a transmission electron microscope (TEM) or focused ion beam (FIB) tool to drill or reshape a small hole in a freestanding membrane. Here, we present a novel method to reduce the size of existing nanopores using electron-beam-induced deposition (EBID) of carbon in a conventional scanning electron microscope (SEM). The existing nanopores are etched in a silicon membrane using anisotropic wet etching and can be shrunk down to a few nanometres using EBID. This paper discusses the parameters that influence the rate of shrinking and provides an insight into the underlying mechanism.