Electronics is approaching a major paradigm shift because silicon transistor scaling no longer yields historical energy-efficiency benefits, spurring research towards beyond-silicon nanotechnologies. In particular, carbon nanotube field-effect transistor (CNFET)-based digital circuits promise substantial energy-efficiency benefits, but the inability to perfectly control intrinsic nanoscale defects and variability in carbon nanotubes has precluded the realization of very-large-scale integrated systems. Here we overcome these challenges to demonstrate a beyond-silicon microprocessor built entirely from CNFETs. This 16-bit microprocessor is based on the RISC-V instruction set, runs standard 32-bit instructions on 16-bit data and addresses, comprises more than 14,000 complementary metal-oxide-semiconductor CNFETs and is designed and fabricated using industry-standard design flows and processes. We propose a manufacturing methodology for carbon nanotubes, a set of combined processing and design techniques for overcoming nanoscale imperfections at macroscopic scales across full wafer substrates. This work experimentally validates a promising path towards practical beyond-silicon electronic systems.