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Abstract Hydrogen, the smallest and most abundant element in nature, can be efficiently incorporated within a solid and drastically modify its electronic and structural state. In most semiconductors interstitial hydrogen binds to defects and is known to be amphoteric, namely it can act either as a donor (H⁺) or an acceptor (H⁻) of charge, nearly always counteracting the prevailing conductivity type. Here we demonstrate that hydrogenation resolves an outstanding challenge in chalcogenide classes of three-dimensional (3D) topological insulators and magnets — the control of intrinsic bulk conduction that denies access to quantum surface transport, imposing severe thickness limits on the bulk. With electrons donated by a reversible binding of H⁺ions to Te(Se) chalcogens, carrier densities are reduced by over 10²⁰cm⁻³, allowing tuning the Fermi level into the bulk bandgap to enter surface/edge current channels without altering carrier mobility or the bandstructure. The hydrogen-tuned topological nanostructures are stable at room temperature and tunable disregarding bulk size, opening a breadth of device platforms for harnessing emergent topological states.