Hydrogen pick-up leading to hydride formation is often observed in commercially pure Ti (CP-Ti) and Ti-based alloys prepared for microscopic observation by conventional methods, such as electro-polishing and room temperature focused ion beam (FIB) milling. Here, we demonstrate that cryogenic FIB milling can effectively prevent undesired hydrogen pick-up. Specimens of CP-Ti and a Ti dual-phase alloy (Ti-6Al-2Sn-4Zr-6Mo, Ti6246, in wt.%) were prepared using a xenon-plasma FIB microscope equipped with a cryogenic stage reaching −135 °C. Transmission electron microscopy (TEM), selected area electron diffraction, and scanning TEM indicated no hydride formation in cryo-milled CP-Ti lamellae. Atom probe tomography further demonstrated that cryo-FIB significantly reduces hydrogen levels within the Ti6246 matrix compared with conventional methods. Supported by molecular dynamics simulations, we show that significantly lowering the thermal activation for H diffusion inhibits undesired environmental hydrogen pick-up during preparation and prevents pre-charged hydrogen from diffusing out of the sample, allowing for hydrogen embrittlement mechanisms of Ti-based alloys to be investigated at the nanoscale.