Intentionally disordered metal–organic frameworks (MOFs) display rich functional behaviour. However, the characterisation of their atomic structures remains incredibly challenging. X-ray pair distribution function techniques have been pivotal in determining their average local structure but are largely insensitive to spatial variations in the structure. Fe-BTC is a nanocomposite MOF, known for its catalytic properties, comprising crystalline nanoparticles and an amorphous matrix. Here, we use scanning electron diffraction to first map the crystalline and amorphous components to evaluate domain size and then to carry out electron pair distribution function analysis to probe the spatially separated atomic structure of the amorphous matrix. Further Bragg scattering analysis reveals systematic orientational disorder within Fe-BTC’s nanocrystallites, showing over 10° of continuous lattice rotation across single particles. Finally, we identify candidate unit cells for the crystalline component. These independent structural analyses quantify disorder in Fe-BTC at the critical length scale for engineering composite MOF materials.