All data files related to the publications, reaction conditions, and characterization equipment are discussed in detail in the publication. Kinetic behavior related to the Pd agglomerates, sintered Pd particles, Lindlar and BASF LF200 catalysts for the catalytic hydrogenation of 3-hexyn-1-ol can be found in the data sets. It includes the corresponding raw Excel file showing H2 pressure and temperature variation versus time in addition to the GC files, activity, and selectivity data sheets, and characterization results including elemental analysis, HAADF-STEM, SEM, XRD, and CO chemisorption. All Nomenclatures are set as referred to in the publication. This study showed that by sintering the Pd agglomerates produced via the microemulsion synthesis method, it is possible to reduce the overhydrogenation rate of the alkynols by sintering and fusion of the Pd species at elevated temperatures. It was tried at different temperatures (473, 623 and 723 K) and it was shown that at a rather similar kinetic behavior (99.99 % conversion and 85-89 % selectivity to cis-hexenol), the sintered Pd aggregates could stay selective despite a catalytic surface area about 7 times larger than that of the Pd agglomerates. This emphasizes the role of low-coordinated edge and corner sites on the final selectivity of the cis-alkenol product and demonstrates that thermal sintering reduces the number of non-selective sites without any need for toxic or organic doping agents or modifiers.