Metal–organic frameworks (MOFs) have been a promising material for many applications, e.g., photocatalysis, luminescence-based sensing, optoelectronics, and electrochemical devices, due to their tunable electronic properties through linker functionalization. In this work, we investigate the effect of mixed organic linkers on the bandgap modulation of polymorphic zirconium-based MOFs, UiO-66 and MIL-140A using density functional theory (DFT) calculations. We show that the electronic properties of both MOFs are in contrast to Vegard’s law for semiconductors, that is, mixed-linker systems exhibit bandgaps not intermediate within the range of single-linker systems. Calculations of the total and partial density of states revealed the formation of mid-gap states in mixed-linker MOFs, causing the bandgap reduction. Interestingly, although both MOFs have similar composition, the effect is more significant in MIL-140A than in UiO-66. This is due to the presence of π–π stacking interactions in MIL-140A, which does not occur in UiO-66. The simulation results reveal a direct relationship between the strength of π–π interactions and the bandgap. This illustrates that distinct structural features, particularly the orientation of organic linkers can give rise to different consequences in bandgap modulation. Moreover, this computational work highlights the possibility to engineer the electronic properties of MOFs through a mixed-linker approach.