Defects in hydrogenated amorphous silicon are reduced by low-energy ion treatments and optional annealing. The treatments leave strongly-bonded hydrogen and other passivants in place, but increase the mobility of loosely-bonded and interstitially trapped hydrogen that would otherwise form unwanted two-level systems (TLS). The mobilized hydrogen atoms may be attracted to unused passivation sites or recombined into H2 gas and diffuse out of the deposited layer. The treatments also increase the density of the material. The optional anneal may partially crystallize the layer, further densify the layer, or both. The reduced number of defects and the increased crystallinity reduce the loss tangent of amorphous silicon dielectrics for superconducting microwave devices.