The presence and variation of chemical functionality and defects in crystalline materials, such as metal-organic frameworks (MOFs), have tremendous impact on their properties. Finding a means of identifying and characterizing this chemical diversity is an important ongoing challenge. This task is complicated by the characteristic problem of bulk measurements only giving a statistical average over an entire sample, leaving uncharacterized any diversity that might exist between crystallites or even within individual crystals. Here, we show that by using fluorescence imaging and lifetime analysis, both the spatial arrangement of functionalities and the level of defects within a multivariable MOF crystal can be determined for the bulk as well as for the individual constituent crystals. We apply these methods to UiO-67 to study the incorporation of functional groups and their consequences on the structural features. We believe that the potential of the techniques presented here in uncovering chemical diversity in what is generally assumed to be homogeneous systems can provide a new level of understanding of materials properties.