Grape canes, the main byproducts of the viticulture industry, contain high-value bioactive phenolic compounds, whose application is limited by their instability and poorly solubility in water. Encapsulation in cyclodextrins allows these drawbacks to be overcome. In this work, a grape cane pilot-plant extract (GC_PPE) was encapsulated in hydroxypropyl beta-cyclodextrin (HP-β-CD) by a spray-drying technique and the formation of an inclusion complex was confirmed by microscopy and infrared spectroscopy. The phenolic profile of the complex was analyzed by LC-ESI-LTQ-Orbitrap-MS and the encapsulation efficiency of the phenolic compounds was determined. A total of 42 compounds were identified, including stilbenes, flavonoids, and phenolic acids, and a complex of (epi)catechin with β-CD was detected, confirming the interaction between polyphenols and cyclodextrin. The encapsulation efficiency for the total extract was 80.5 ± 1.1%, with restrytisol showing the highest value (97.0 ± 0.6%) and (E)-resveratrol (32.7 ± 2.8%) the lowest value. The antioxidant capacity of the inclusion complex, determined by ORAC-FL, was 5300 ± 472 µmol TE/g DW, which was similar to the value obtained for the unencapsulated extract. This formulation might be used to improve the stability, solubility, and bioavailability of phenolic compounds of the GC_PPE for water-soluble food and pharmaceutical applications.