A protocol was developed to distinguish between well‐defined molecular and nanoparticle‐based catalysts for the Pd‐catalyzed semihydrogenation reaction of alkynes to Z‐alkenes. The protocol applies quantitative partial poisoning and dynamic light scattering methods, which allow the institution of additional validation experiments. For the quantitative partial poisoning method, tetramethylthiourea (TMTU) was developed as an alternative for the standard poison ligand CS2, and was found to be superior in its applicability. The protocol and the TMTU poison ligand were validated using the well‐described [PdII(phenanthroline)]‐catalyzed copolymerization of styrene and CO, confirming that this system is clearly operating as a well‐defined molecular catalyst. The protocol was subsequently applied to three catalyst systems used for the semihydrogenation of alkynes. The first was proposed to be a molecular [Pd0(IMes)] catalyst that uses molecular hydrogen, but the data gathered for this system, following the new protocol, clearly showed that nanoparticles (NPs) are catalytically active. The second catalyst system studied was an N‐heterocyclic carbene (NHC) Pd system for transfer semihydrogenation using formic acid as the hydrogen source, which was proposed to operate through an in situ generated molecular [Pd0(IMes)] catalyst in earlier studies. The investigations showed that only a small fraction of the Pd added becomes active in the catalytic reaction and that NPs are formed. However, despite these findings, a clear distinction between catalytic activity of NPs versus a molecular catalyst could not be made. The third investigated system is based on a [PdII(IMes)(η3‐allyl)Cl] precatalyst with additive ligands. The combined data gathered for this system are multi‐interpretable, but suggest that a partially deactivated molecular catalyst dominates in this reaction.