Covalent organic frameworks (COFs) are new class of organic porous materials with tunable pore size and low weight density, demonstrating remarkable potential applications in gas storage, gas separation, and catalysis. The inherent periodic porosity of COF monolayers (MLs) establishes anchoring sites for single atoms. Using first-principles calculations, we study the structural and electronic properties of atom-embedded C6N6 and B6O6 MLs. Subsequently, the intercalation of atoms between C6N6 and B6O6 bilayers (BLs) and their heterostructure (HTS) are investigated. Our findings show the significant effects of embedded atoms on the structural parameters of the host material. Notably, the Li atom anchors within the pore region of C6N6 ML without forming bonds, while it establishes two σ bonds with O atoms in B6O6 ML. The Cs atom forms six bonds in both MLs and resides between layers in BLs. In the HTS, the Cs atom forms six bonds with N atoms of the C6N6 layer, positioning in the middle of the layers. Calculations reveal that Li and Cs atoms induce a red shift in energy, leading to a semiconductor–metal transition. Conversely, the insertion of an F atom induces a blue shift in energy, creating a midgap state at the Fermi energy.