In this paper, a process for generating collagen-yttria-stabilized amorphous zirconia hybrid scaffolds by introducing acetylacetone-inhibited zirconia precursor nanodroplets into a poly(allylamine)-coated collagen matrix is reported. This polyelectrolyte coating triggers intrafibrillar condensation of the precursors into amorphous zirconia, which is subsequently transformed into yttria-stabilized zirconia after calcination. These findings represent a new paradigm in the synthesis of non-naturally occurring collagen-based hybrid scaffolds under alcoholic mineralizing conditions.