Research on permanently porous nanomaterials has gripped the attention of materials chemists for decades. Mesoporous silica nanoparticles (MSNs) and metal-organic frameworks (MOFs) are two of the most studied classes of materials in this field. Recently, explorations into embedding MOFs within the mesopores of MSNs have aimed to create composites that are greater than the sum of their parts. While initial progress has been promising, it has become clear that the characterization of these MOF@MSN composite materials represents a significant challenge that is often overlooked, leading to an unfortunate ambiguity in the field. The greatest difficulty lies in determining whether the product of a synthesis is simply a physical mixture of the two materials or truly the targeted composite, with MOF exclusively crystallized in the pores or on the surfaces of the MSN. This challenge is aggravated by the dramatically different porosity and composition of the components, often resulting in ambiguous information from common characterization techniques. This Viewpoint will address this challenge by calling attention to the mentioned issues and proposing a standardized approach to characterizing these materials. In particular, the use of powder X-ray diffraction, gas physisorption, and electron microscopy with systematic control experiments and data analysis is outlined. This approach can provide the information needed to clearly validate the architecture of an apparent MOF@MSN composite.