Mixed-linker zeolitic imidazolate frameworks (ZIFs) are important candidate materials for gas separation. By changing the linker content, their pore size can be tuned, offering the potential to regulate diffusion and adsorption. An important factor affecting these properties in mixed-linker ZIFs is the linker distribution, which is difficult to characterize. In this study, the microscopic linker distribution in mixed-linker ZIF-8/ZIF-90, with respectively methyl and carboxaldehyde functionalization, is elucidated via computational Raman spectroscopy. It is shown that the typical Raman band associated with the carboxaldehyde linker is shifted due to a change in hydrogen-bonding behavior. This insight allows one to explain the microscopic linker distribution in experimental mixed-linker structures.