A hybrid adsorbent-catalytic nanostructured material consisting of aminopropyl groups and nickel nanoparticles immobilized in mesoporous silica nanoparticles (AP-Ni-MSN) was employed to selectively capture free fatty acids (FFAs) and convert them into saturated hydrocarbons. The working principle of these sorbent-catalytic particles was initially tested in the hydrogenation of oleic acid. Besides providing selectivity for the capture of FFAs, the adsorbent groups also affected the selectivity of the hydrogenation reaction, shifting the chemistry from hydrocracking-based (Ni) to hydrotreating-based and improving the carbon economy of the process. This approach was ultimately evaluated by the selective sequestration of FFAs from crude microalgal oil and their subsequent conversion into liquid hydrocarbons, demonstrating the suitability of this design for the refinery of renewable feedstocks.