The catalytic utility of [RuL¹(CO)₂I₂] (1), containing an annelated π-conjugated imidazo-naphthyridine-based mesoionic carbene (MIC) ligand (L¹), is evaluated for E-selective alkyne semihydrogenation. The precatalyst 1, in combination with 2 equiv of AgBAr^F, semihydrogenates a broad range of internal alkynes with molecular hydrogen (5 bar) in water. (E)-Alkenes are accessed in high yields, and a number of reducible functional groups are tolerated. A chelate MIC ligand and two cis carbonyls provide a well-defined platform at the Ru center for hydrogenation and isomerization. The loss of two iodides and the presence of two carbonyls render the Ru center electron deficient and thus the formation of metal vinylidenes with terminal alkynes is avoided. This is leveraged for the semihydrogenation of terminal alkynes by the same catalytic system in isopropyl alcohol. Reaction profile, isomerization, kinetic, and DFT studies reveal initial alkyne hydrogenation to a (Z)-alkene, which further isomerizes to an (E)-alkene via metal-catalyzed Z → E isomerization.