The exploration and use of deuteriodifluoromethyl heteroatom groups (X‐CF2D) has been limited by persistent challenges, including the unavailability of CF2D precursor reagents, as well as safety, scalability, and environmental concerns associated with conventional batch‐mode syntheses. In this study, we report the use of atom‐efficient and cost‐effective R‐22 gas (ClCF2H) in continuous flow for the rapid installation of CF2H and CF2D groups on heteroatom centers. However, the intrinsic nucleophilic substitution between heteroatom anions and ClCF2H decreases the deuterium incorporation levels. Notably, a judiciously designed continuous flow system proves to suppress the previously unavoidable SN2 reaction and allows for the selective carbene coupling to generate X‐CF2D products with high deuterium incorporation levels up to 96%. Our continuous flow systems provide a broad scope of X‐CF2H and X‐CF2D products (X = S, O, N) within a short residence time of 5 minutes and scalability is also demonstrated.