We report a new methodology to synthesize thin films with exceptional microstructural control via systematic, in-situ seeding of nanocrystals into amorphous precursor films. When the amorphous films are subsequently crystallized by thermal annealing, the nanocrystals serve as preferential grain nucleation sites and control their micro/nanostructure. We demonstrate the capability of this methodology by precisely tailoring the size, geometry and spatial distribution of nanostructured grains in structural (TiAl) as well as functional (TiNi) thin films. This synthesis methodology is likely to be applicable to other amorphously grown materials and enables explicit microstructural control in a wide spectrum of thin films/coatings. IMPACT STATEMENT This paper describes a novel synthesis methodology to precisely tailor the microstructure of thin films and reveals the mechanisms underlying this methodology using in-situ TEM annealing experiments.