Halloysite nanotube supported ruthenium catalyst was prepared by an easy and reproducible in situ bottom up approach. Ruthenium (III) chloride was reduced by sodium borohydride in the presence of halloysite nanotubes dispersed in water. Several analyses confirm the immobilization of ruthenium particles onto the aluminosilicate support. The synthesized catalyst was then tested in the hydrogenation of 1-hexadecene, a highly hydrophobic compound, in aqueous medium using cyclodextrins as mass transfer additives. The catalytic activity deeply depended on the nature of the cyclodextrin. Best results were obtained with randomly methylated β-cyclodextrin. The catalytic system was also evaluated in the hydrogenation of biosourced long chain alkenes such as fatty acid methyl esters and vegetable oils and showed high activities in mild reaction conditions.