Disclosed are methods for co-integration of active and passive photonic devices on a planarized silicon-based photonics substrate. In one aspect, a method is disclosed that includes providing a planarized silicon-based photonics substrate comprising a silicon waveguide structure, depositing a dielectric layer over the planarized silicon-based photonics substrate, selectively etching the dielectric layer, thereby exposing at least a portion of the silicon waveguide structure, selectively etching the exposed portion of the silicon waveguide structure to form a template, using the silicon waveguide structure as a seed layer to selectively grow in the template a germanium layer that extends above the dielectric layer, and planarizing the germanium layer to form a planarized germanium layer, wherein the planarized germanium layer does not extend above the dielectric layer.