Recently, the use of mixtures of organic-building-block linkers has given chemists an additional degree of freedom for engineering metal-organic frameworks (MOFs) with specific properties; however, the poor characterization of the chemical complexity of such MixMOF structures by conventional techniques hinders the verification of rational design. Herein, we describe the application of a technique known as photothermal induced resonance to individual MixMOF microcrystals to elucidate their chemical composition with nanoscale resolution. Results show that MixMOFs isoreticular to In-MIL-68, obtained either directly from solution or by postsynthetic linker exchange, are homogeneous down to approximately 100 nm. Additionally, we report a novel in situ process that enables the engineering of anisotropic domains in MOF crystals with submicron linker-concentration gradients.