Abstract Single‐atom catalysts (SACs) based on phthalocyanine‐derived (MPc) structures offer a convenient platform to study the interplay between local coordination environments and catalytic activity. In this work, we synthesized Mo‐ and Re‐based polymeric phthalocyanine materials and treated them in H 2 S flow at 550 °C and 750 °C to obtain three catalyst families: pristine MN 4 (M = Mo, Re), sulfided MN 4 S x single‐atom materials, and nanodispersed MS 2 ‐like clusters. The presence of single atomic sites and nanoclusters was attested by conventional techniques and by Scanning Transmission Electron Microscopy‐Annular Dark Field imaging (STEM‐ADF). Operando X‐ray Absorption Spectroscopy (XAS) combined with chemometric methods revealed progressive transformation of single‐atom sites into sulfide species and allowed direct observation of coordination evolution and metal atoms agglomeration. The catalytic activity of these systems was evaluated in Hydrogen Evolution (HER), Oxygen Reduction (ORR), and Hydrodesulfurization (HDS). A strong structure–activity relationship was established: fully single‐atomic MN 4 sites exhibited no activity in HER or HDS, but displayed measurable ORR performance, favoring a four‐electron pathway to water. After sulfidation at 550 °C the catalysts remain single‐atomic and acquire sulfur in the coordination sphere of metal, forming MN 4 S x sites, but still are inactive in HER and HDS. Only upon high‐temperature sulfidation (750 °C), the coordination polymer framework is destroyed, MoS 2 (ReS 2 ) slabs are formed, HER and HDS activity emerges, whereas ORR selectivity shifts from a 4‐electron to a 2‐electron pathway, favoring H 2 O 2 formation. This work underscores both the catalytic potential and the limitations of single‐atom MPc catalysts, highlighting the versatility of active site structures required for different processes.