Abstract Understanding the physical properties and controlling the generation of intrinsic and extrinsic defects is central to the technological adoption of 2D materials in devices. Here we identify a charged carbon-hydrogen complex at a chalcogen site (CH_X) as a common, charged impurity in synthetically grown transition metal dichalcogenides (TMDs). This conclusion is drawn by comparing high resolution scanning probe microscopy measurements of nominally undoped and intentionally carbon doped TMD samples. While CH impurity densities in undoped CVD-grown WS₂ and MOCVD-grown WSe₂ can range anywhere from parts per million to parts per thousand, CH densities in the percentage levels were selectively generated by a post-synthetic methane plasma treatment. Our study indicates that methane plasma treatment is a selective and clean method for the controlled introduction of a charged carbon-hydrogen complex at a surface chalcogen site, a defect that is commonly present in synthetic TMDs.