Composite materials, consisting of a metal–organic framework (MOF) and a guest molecule, further denoted as guest@MOF composites, have gained strong interest due to the guest-induced tunability of the host properties, for example in sensing or electroconductivity applications. However, decoding the complexity of these guest@MOF composites and extracting structure-performance relationships are far from trivial and require the use of a gamut of characterization tools. In this work, we use various micro-spectroscopic tools both under static (ex situ) and dynamic (in situ) conditions to map the properties and diffusion behavior of TCNQ (7,7,8,8-tetracyanoquinodimethane) as a guest molecule in single HKUST-1 crystals as the host. Raman micro-spectroscopy allowed us to map the spatial distribution of TCNQ within HKUST-1 single crystals, thereby revealing a heterogeneous distribution of TCNQ after initial TCNQ-infiltration, concentrated at the crystal edges, and a homogeneous redistribution upon water vapor treatment. These insights are correlated to I–V scans at different temperatures and to electrochemical impedance spectroscopy (EIS), which allowed us to verify the different contributions to conductivity. These data showed changes in electrical conductivity after exposing the sample to moisture and air. In situ FT-IR micro-spectroscopy during treatment with moisturized nitrogen gas suggests lower transient diffusion rates for water inside TCNQ@HKUST-1 relative to pristine HKUST-1, likely due to steric hindrance of the pore-filling TCNQ molecules in the HKUST-1 framework. The application of micro-spectroscopic techniques is crucial to uncovering MOF intracrystal heterogeneities and yielding rationally-derived instructions for the improved design of guest@MOF systems.