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Abstract Geopolymers, as a potentially environmentally friendly alternative to Portland cement, are increasingly attracting attention in the construction industry. Various methods have been applied for customizing the properties of geopolymers and improving their commercial viability. One of the promising methods for refining the properties of geopolymers such as their toughness is the use of short fibers. The effectiveness of a high‐strength short fiber in the geopolymer matrix is largely dependent on the interfacial bonding between the fiber and its surrounding matrix. While the importance of this interfacial chemistry is highlighted in the literature, the characteristics of this bonding structure have not been fully understood. In this paper, we aim to investigate the bonding mechanism between the carbon fiber and metakaolin‐based geopolymer matrix. For the first time, the existence and nature of the chemical bonding at the interfacial region (interphase) between carbon fiber and geopolymer matrix has been revealed. X‐ray pair distribution function computed tomography (PDF‐CT), field emission‐scanning electron microscopy imaging, and nanoindentation techniques are employed to discern the chemo‐mechanical properties of the interphase. PDF‐CT results show the emergence of a new atom–atom correlation at the interfacial region (around 1.82 Å). This correlation is a characteristic of interfacial bonding between the fiber and its surrounding matrix, where the existence of chemical linkages (potentially^VAl‐O‐C) between fibers and the matrix contributes to the adhesion between the two constituents making up the composite. Due to such chemical bonding, the nanomechanical properties of the interfacial region fall between that of the carbon fiber and geopolymer. The combination of advanced techniques is proved useful for enhancing our understanding of the interfacial chemistry between fibers and the binding matrix. This level of knowledge facilitates the engineering of composite systems through the manipulation of their nanostructure.