We demonstrate the creation of a spin-1/2 state via the atomically controlled generation of magnetic carbon radical ions (CRIs) in synthetic two-dimensional transition metal dichalcogenides. Hydrogenated carbon impurities located at chalcogen sites introduced by chemical doping are activated with atomic precision by hydrogen depassivation using a scanning probe tip. In its anionic state, the carbon impurity exhibits a magnetic moment of 1 μB resulting from an unpaired electron populating a spin-polarized in-gap orbital. By inelastic tunneling spectroscopy and density functional theory we show that the CRI defect states couple to a small number of vibrational modes, including a local, breathing-type mode. The electron-phonon coupling strength critically depends on the spin state and differs for monolayer and bilayer WS2. These carbon radical ions in TMDs comprise a new class of surface-bound, single-atom spin-qubits that can be selectively introduced, are spatially precise, feature a well-understood vibronic spectrum, and are charge state controlled.