Segmented polymers, such as polyether block amide (PEBA), exhibit unique properties due to the combination of different segments. PEBA consists of soft polyester and rigid polyamide blocks, enabling its use in various industrial applications, including membrane technologies. In this study, PEBA membranes modified with a holmium-based metal–organic framework (Ho-1,3,5-H3btc) were developed for enhanced pervaporation separation of water/isopropanol and water/phenol mixtures. The effect of 1–7 wt.% Ho-1,3,5-H3btc content variation and the selection of a porous substrate (commercial from fluoroplast F42L (MFFC) and developed membranes from polyvinylidene fluoride without (PVDF) and with a non-woven polyester support (PVDF-s)) on dense and/or supported membrane properties, respectively, was investigated. The dense and supported PEBA/Ho-1,3,5-H3btc membranes were studied by use of Fourier transform infrared spectroscopy, scanning electron and atomic force microscopies, swelling measurements, and pervaporation experiments. The supported membrane from PEBA with 5 wt.% Ho-1,3,5-H3btc applied onto the PVDF-s substrate exhibited optimal pervaporation performance: a 1040 g/(m2h) permeation flux and a 5.2 separation factor in water/phenol (1 wt.%) mixture separation at 50 °C due to optimal values of roughness, swelling degree, and selective layer thickness. This finding highlights the potential of incorporating Ho-1,3,5-H3btc into PEBA for developing high-performance pervaporation membranes.