The blend of polyetheretherketone (PEEK) and polybenzimidazole (PBI) produces a high-performance blend (PPB) that is a potential replacement material in several industries due to its high temperature stability and desirable tribological properties. Understanding the nanoscale structure and interface of the two domains of the blend is critical for elucidating the origin of these desirable properties. Whilst achieving the physical characterisation of the domain structures is relatively uncomplicated, the elucidation of structures at the interface presents a significant experimental challenge. In this work, we combine atomic force microscopy (AFM) with an IR laser (AFM-IR) and thermal cantilever probes (nanoTA) to gain insights into the chemical heterogeneity and extent of mixing within the blend structure for the first time. The AFM-IR and nanoTA measurements show that domains in the blend are compositionally different from those of the pure PEEK and PBI polymers, with significant variations observed in a transition region several microns wide in proximity to domain boundary. This strongly points to physical mixing of the two components on a molecular scale at the interface. The versatility intrinsic to the combined methodology employed in this work provides nano- and microscale chemical information that can be used to understand the link between properties of different length scales across a wide range of materials.