In this work, we performed a comprehensive hybrid-level computational study of transition metal intercalation in triazinebenzene-boroxine 2D COFs for catalytic, magnetic, and electronic/spintronic property enhancement. We describe the structural and electronic properties of the pristine bilayer 2D COF. This structure presents insulating electronic character (bandgap of 3.40 eV). In this material, carbon atoms are the main contributors to the electronic states surrounding the Fermi level. Next, we generated sixty-three intercalated bilayer structures with nine first-row transition metals. Our analyses reveal that the type, concentration, and position of intercalants changes their structural, magnetic, and electronic features. Structurally, intercalation results in changes in the interlayer distance, which can be directly related to interaction strength between the transition metals and the bilayer. The structural analysis was complemented with a binding energy analysis, where we observe that transition metal intercalation is energetically preferred at the centroid of benzene rings, followed by triazine and boroxine. This indicates that-generally-during intercalation, the centroid of benzene rings will be populated first, followed by triazine, and finally boroxine. Magnetically, we observe a wide range of stable spin configurations (FM, FiM, AFM, NM), which depend on the type, position, and concentration of intercalants. This wide range of magnetic features allows to fine-tune and enhance 2D COFs' features for photocatalytic, electronic, and spintronic applications. In general, we find that transition metal d-orbitals have important contributions to the density of states around the Fermi level and can even promote the contribution of C, N, B, and O atoms around the Fermi level. Within our sixty-three intercalated bilayer 2D COFs, we find that twenty-four of our materials are conductors in at least one of their spin channels, while the rest are semiconductors or insulators with a bandgap ranging from 0.2 to 3.24 eV. In terms of photocatalysis, our absolute spin-polarized band edge alignment shows that all of our semiconducting materials have a band alignment suitable for hydrogen reduction through photoexcited electrons, and one of our materials (Ni-01a) has a band alignment suitable for oxygen evolution photocatalysis. Within the semiconductor COFs, we find three (Cr-03, Ti-03, and V-03) that have direct bandgaps that fall within the visible range; therefore, they are ideal for optoelectronics. Finally, we explore the spintronic properties of our materials, where we observe that eighteen of them (Co-03, Cr-01a, Cr-01b, Cr-04a, Cu-01a, Cu-01b, Fe-04b, Fe-05, Ni-03, Ni-04a, Ni-04b, Ni-05, Sc-01a, Sc-01b, Sc-04b, Ti-01a, Ti-02, and Ti-05) present half metal behavior, five of them (Co-04a, Co-04b, Cr-02, Mn-04a, and V-01a) have appropriate band alignments for their use as half semiconductors, and eleven of them (Cu-02, Fe-01a, Fe-01b, Mn-01a, Mn-01b, Sc-02, Ti-04a, Ti-04b, V-02, V-04b and V-05) have potential application as bipolar magnetic semiconductors. However, bilayer BMSs present large gaps within their band structure below the VBM, which inhibits the movement of electrons within the material. To remedy this issue and as proof of concept, we added another fully intercalated COF layer to the V-05 structure, which provided more intermediate electronic density levels while preserving its bipolar magnetic semiconducting character. In general, this work provides a new architecture of isolated bilayer and trilayer TM-intercalated 2D COFs, which have the potential to be used in a wide array of fields, including catalysis, optoelectonics, and spintronics.