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The efficient extraction of phenols from grapes is an important step for their reliable quantification. The aim was to optimise the lyophilisation process and the extraction of phenols from grape skins and seeds. The phenol extraction yield from lyophilised tissues was investigated with different accelerated solvent extraction (ASE) operating conditions. Skins and seeds were separated from frozen berries and lyophilised without being ground. The weight loss during lyophilisation was followed daily. Phenols were extracted from lyophilised, cryo-ground seeds and skins with ASE at room temperature and 10.3 MPa using 80% aqueous acetone and 60% aqueous methanol. The effects of ASE operational parameters (the number of extraction cycles (ECs) and static time (ST) duration) were investigated. The yield of extracted phenols was evaluated spectrophotometrically by determining total phenolic index at 280 nm (TPI). The weight of skins and seeds significantly dropped after 24 h of lyophilisation and continued to decrease, although not significantly, up until the 9th day. The optimal lyophilisation time was estimated to be 3 days and 5 days for skins and seeds, respectively. The phenol extraction yield was significantly affected after changes of ASE conditions. Based on TPI, the optimal ASE conditions were as follows: (i) lyophilised seeds—eight ECs with 10 min ST using aqueous acetone and then four ECs with 20 min ST using aqueous methanol; (ii) lyophilised skins—eight ECs with 1 min ST using aqueous acetone and then one EC with 20 min ST using aqueous methanol.