Innovative cobalt and nickel catalytic materials containing metal nanoparticles immobilized into the inner tubes of pristine halloysite, a naturally occurring nanoclay, and their application in hydrogenation reactions of a large variety of substrates from biomass and industrial wastes are described herein. The catalytic materials with a high metal loading (>24 wt.%) were prepared by a one-pot two-steps procedure in the absence of additional stabilizers, leading to metal nanoparticles essentially confined into the support lumen (constituted of aggregates of small nanoparticles) as a result of the privileged electrostatic interactions between aluminols and metal acetate salts (Ni(OAc)2, Co(OAc)2). Both catalytic materials, Ni/Hal and Co/Hal, gave different chemoselectivities towards the reduction of unsaturated functional groups (carbonyl, C=C, nitrile) under solvent-free conditions, and thus affording selectively added-value compounds depending on the nature of the metal. In particular, the squalene hydrogenation monitoring permitted to identify the partial hydrogenated products and estimate the partial turnover numbers and frequencies, achieving a cumulative TON of 110 and TOF of 151 h-1 using the most active catalytic system, i.e. Ni/Hal.