The combination of porous reticular frameworks and nanocrystals (NCs) offers a rich playground to design materials with functionalities, which are beneficial for a large variety of applications. Achieving compositional and structural tunability of these hybrid platforms is not trivial, and new approaches driven by the understanding of their formation mechanism are needed. Here, we present a synthetic route to encapsulate NCs of various sizes, shapes, and compositions in the microporous imine-linked covalent organic framework (COF) LZU1. The tunable NC@LZU1 core-shell hybrids are synthesized by combining colloidal chemistry and homogeneous microwave-assisted syntheses, an approach that allows tailoring of the shell thickness while ensuring COF crystallinity in the presence of the NCs. The uniform morphologies of these new composite materials along with their colloidal nature enable insights into their formation mechanism. Having learned that the COFs heterogeneously nucleate on the NC seeds, we further expand the synthetic approach by developing a step-by-step encapsulation strategy. Here, we gain control over the spatial distribution of various NCs within multilayered NC@LZU1@Nc@LZU1 core-shell-core-shell hybrids and also form yolk-shell nanostructures. The synthetic route is general and applicable to a broad variety of NCs (with catalytic, magnetic, or optical properties), thus revealing a new way to impart functionalities to COFs.