Several ruthenium(IV) complexes have been tested as potential catalysts for the isomerization of estragole into anethole using water and glycerol as alternative green reaction media. Best results in terms of activity and E-selectivity were obtained with the dimeric species [{RuCl(μ-Cl)(η³:η³-C₁₀H₁₆)}₂] (C₁₀H₁₆ = 2,7-dimethylocta-2,6-diene-1,8-diyl) and the mononuclear derivative [RuCl₂(η³:η³-C₁₀H₁₆){P(OMe)₃}]. In particular, using a ruthenium loading of 1 mol%, almost quantitative and stereoselective formation of trans-anethole (trans/cis ratios = 99 : 1) could be reached at 80 °C in short times (5–30 min) employing water–MeOH (EtOH) or glycerol–MeOH (EtOH) mixtures (1 : 1 v/v) as solvent. Recyclability issues have also been addressed.