AbstractSingle‐atom heterogeneous catalysts (SACs) hold promise as sustainable alternatives to metal complexes in organic transformations. However, their working structure and dynamics remain poorly understood, hindering advances in their design. Exploiting the unique features of droplet‐based microfluidics, we present the first in‐situ assessment of a palladium SAC based on exfoliated carbon nitride in Suzuki–Miyaura cross‐coupling using X‐ray absorption spectroscopy. Our results confirm a surface‐catalyzed mechanism, revealing the distinct electronic structure of active Pd centers compared to homogeneous systems, and providing insights into the stabilizing role of ligands and bases. This study establishes a valuable framework for advancing mechanistic understanding of organic syntheses catalyzed by SACs.