Covalent organic frameworks (COFs) are an emerging class of porous organic polymers that have been utilized as scaffolds for anchoring metal active species to act as heterogeneous catalysts. Though several examples of such COFs exist, a thorough experimental and computational analysis on such catalysts is limited. In this work, a series of two-dimensional (2D) imine COFs (TTA–DFB COF (N), TTA–TBD COF (N∧O), and TTA–DFP COF(N∧N)) were synthesized by using suitable building units to obtain three different coordination sites (N, N∧O, and N∧N). These were post-modified with Pd(II) to catalyze the Suzuki–Miyaura coupling reaction. Pd@TTA–DFB COF, where Pd(II) was coordinated to N sites, showed the fastest reactivity and lower stability. Pd@TTA–DFP COF showed highest stability but slowest reactivity. Pd@TTA–TBD COF was the best among the three with both high stability and fast reactivity. By combining both experimental and computational results, we conclude that the Pd(II) to Pd(0) reduction is a key step in the difference between the catalytic reactivities of the three COFs. This study demonstrates the importance of the building block approach to design COFs for efficient heterogeneous catalysis and to understand the fate of the reaction profile.