The last decade has witnessed the rapid development of inkjet printing as an attractive bottom-up microfabrication technology due to its simplicity and potentially low cost. The wealth of printable materials has been key to its widespread adoption in organic optoelectronics and biotechnology. However, its implementation in nanophotonics has so far been limited by the coarse resolution of conventional inkjet-printing methods. In addition, the low refractive index of organic materials prevents the use of “soft-photonics” in applications where strong light confinement is required. This study introduces a hybrid approach for creating and fine tuning high-Q nanocavities, involving the local deposition of an organic ink on the surface of an inorganic 2D photonic crystal template using a commercially available high-resolution inkjet printer. The controllability of this approach is demonstrated by tuning the resonance of the printed nanocavities by the number of printer passes and by the fabrication of photonic crystal molecules with controllable splitting. The versatility of this method is evidenced by the realization of nanocavities obtained by surface deposition on a blank photonic crystal. A new method for a free-form, high-density, material-independent, and high-throughput fabrication technique is thus established with a manifold of opportunities in photonic applications.