Abstract: The need to develop green and cost-effective industrial catalytic processes has led to growing interest in preparing more robust, efficient, and selective heterogeneous catalysts at a large scale. In this regard, microwave-assisted synthesis is a fast method for fabricating heterogeneous catalysts (including metal oxides, zeolites, metal–organic frameworks, and supported metal nanoparticles) with enhanced catalytic properties, enabling synthesis scale-up. Herein, the synthesis of nanosized UiO-66-NH2 was optimized via a microwave-assisted hydrothermal method to obtain defective matrices essential for the stabilization of metal nanoparticles, promoting catalytically active sites for hydrogenation reactions (760 kg·m–3·day–1 space time yield, STY). Then, this protocol was scaled up in a multimodal microwave reactor, reaching 86% yield (ca. 1 g, 1450 kg·m–3·day–1 STY) in only 30 min. Afterward, Pd nanoparticles were formed in situ decorating the nanoMOF by an effective and fast microwave-assisted hydrothermal method, resulting in the formation of Pd@UiO-66-NH2 composites. Both the localization and oxidation states of Pd nanoparticles (NPs) in the MOF were achieved using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and X-ray photoelectron spectroscopy (XPS), respectively. The optimal composite, loaded with 1.7 wt % Pd, exhibited an extraordinary catalytic activity (>95% yield, 100% selectivity) under mild conditions (1 bar H2, 25 °C, 1 h reaction time), not only in the selective hydrogenation of a variety of single alkenes (1-hexene, 1-octene, 1-tridecene, cyclohexene, and tetraphenyl ethylene) but also in the conversion of a complex mixture of alkenes (i.e., 1-hexene, 1-tridecene, and anethole). The results showed a powerful interaction and synergy between the active phase (Pd NPs) and the catalytic porous scaffold (UiO-66-NH2), which are essential for the selectivity and recyclability.