Nanostructuring earth-abundant metals as single atoms or clusters of controlled size on suitable carriers opens new routes to develop high-performing heterogeneous catalysts, but resolving speciation trends remains challenging. Here, we investigate the potential of low-nuclearity iron catalysts in the continuous liquid-phase semi-hydrogenation of various alkynes. The activity depends on multiple factors, including the nuclearity and ligand sphere of the metal precursor and their evolution upon interaction with the mesoporous graphitic carbon nitride scaffold. Density functional theory predicts the favorable adsorption of the metal precursors on the scaffold without altering the nuclearity and preserving some ligands. Contrary to previous observations for palladium catalysts, single atoms of iron exhibit higher activity than larger clusters. Atomistic simulations suggest a central role of residual carbonyl species in permitting low-energy paths over these isolated metal centers.