A combined extract from three different interspecific grape crosses was used for the isolation of bioactive stilbenes. High-performance liquid chromatography coupled to hybrid quadrupole time-of-flight (Q-TOF) mass spectrometry was employed for the identification and determination of the analytes. A total of 27 stilbene derivatives were identified with mass accuracy ranging from −1.18 to 3.41 ppm. A subset of 16 compounds (cis/trans-piceid, cis/trans-piceatannol, cis/trans-resveratrol, cis/trans-scirpusin A, cis/trans-ε-viniferin, cis/trans-ω-viniferin, cis/trans-δ-viniferin, and E/Z-miyabenol C) were quantified and compared in the grape stems, seeds, skins, and juice from three different interspecific crosses. The stems and skins were the richest and second richest sources for all targeted stilbenes, respectively. The only compounds found in considerable amounts in grape juice were cis- and trans-piceids. The performance of unit resolution tandem mass spectrometric QqQ system was compared to the Q-TOF mass spectrometer in terms of matrix effects. The detection by QqQ unexpectedly exhibited an elevated matrix effect with a high degree of ion enhancement, especially in samples of grape stems and skins, while the Q-TOF system showed notably lower matrix effects.