The reduction of carbon dioxide (CO₂) into value-added feedstock materials, fine chemicals, and fuels represents a crucial approach for meeting contemporary chemical demands while reducing dependence on petrochemical sources. Optimizing catalysts for the CO₂ reduction reaction (CO₂RR) can entail employing first principles methodology to identify catalysts possessing desirable attributes, including the ability to form diverse products or selectively produce a limited set of products, or exhibit favorable reaction kinetics. In this study, we investigate CO₂RR on bimetallic Cu-based paddlewheel complexes, aiming to understand the impact metal substitution with Mn(II), Co(II), or Ni(II) has on bimetallic paddlewheel metal–organic frameworks. Substituting one of the Cu sites of the paddlewheel complex with Mn results in a more catalytically active Cu center, poised to produce substantial quantities of formic acid (HCOOH) and smaller quantities of methane (CH₄) with a suppressed production of C₂ products such as ethanol (CH₃CH₂OH) or ethylene (C₂H₄). Moreover, the presence of Mn significantly reduces the limiting potential for CO₂ reduction from 2.22 eV on the homo-bimetallic Cu paddlewheel complex to 1.19 eV, thereby necessitating a smaller applied potential. Conversely, within the Co-substituted paddlewheel complex, the Co site emerges as the primary catalytic center, selectively yielding CH₄ as the sole reduced CO₂ product, with a limiting potential of 1.22 eV. Notably, the Co site faces significant competition from H₂ production due to a lower limiting potential of 0.81 eV for hydrogen reduction. Our examination of the Cu–Ni paddlewheel complex, featuring a Ni substituent site, reveals two catalytically active centers, each promoting distinct reductive processes. Both the Ni and Cu sites exhibit a propensity for HCOOH formation, with the Ni site favoring further reduction to CH₄, whereas the Cu site directs the reaction towards methanol (CH₃OH) production. This study holds significance in informing and streamlining future experimental efforts for synthesizing and evaluating novel catalysts with superior capabilities for CO₂ reduction.