In this paper, we report on the phase selectivity in Cr and N co-doped TiO2 (TiO2:Cr,N) sputtered films by means of interface engineering. In particular, monolithic TiO2:Cr,N films produced by continuous growth conditions result in the formation of a mixed-phase oxide with dominant rutile character. On the contrary, modulated growth by starting with a single-phase anatase TiO2:N buffer layer, can be used to imprint the anatase structure to a subsequent TiO2:Cr,N layer. The robustness of the process with respect to the growth conditions has also been investigated, especially regarding the maximum Cr content (<5 at.%) for single-phase anatase formation. Furthermore, post-deposition flash-lamp-annealing (FLA) in modulated coatings was used to improve the as-grown anatase TiO2:Cr,N phase, as well as to induce dopant activation (N substitutional sites) and diffusion. In this way, Cr can be distributed through the whole film thickness from an initial modulated architecture while preserving the structural phase. Hence, the combination of interface engineering and millisecond-range-FLA opens new opportunities for tailoring the structure of TiO2-based functional materials.