In this work, we report on a simple and easy to realize doping geometry by which the color center formation efficiency can be improved significantly in nanocrystalline diamond structures during solid impurity source-assisted microwave plasma enhanced chemical vapor deposition (MWCVD). A vertically aligned solid impurity source immersed into the CVD plasma results in diamond thin film with significantly higher color center related fluorescence signal, than the horizontal and source-free arrangements. Based on the example of negatively charged silicon-vacancy (SiV−) center, we demonstrated that the emission peak intensity of fluorescent nanodiamond structures prepared in such a way can be 7–10 times enhanced without significant alteration of the crystal quality. The observed phenomenon is explained by the increased number of incorporated silicon impurities into the diamond nanocrystals, initiated by the beneficial conditions for the atomization of the vertically aligned impurity source, including the enlarged contact area and the elevated surface temperature. The efficiency of the method was demonstrated for thin films and individual nanocrystal structures as well. The proposed solid-phase doping source geometry can be adapted to other impurities to extend the type or improve the in-situ formation efficiency of impurity related color centers in CVD nanodiamond crystals.