The pisco industry in Peru generates large amounts of grape pomace, which is a natural source of bioactive compounds with potential nutraceutical applications. Hot pressurized liquid extraction (HPLE) with water-ethanol solvent mixtures (20–60%) at high temperatures (100–160◦C) was applied to recover polyphenols from the skin and seeds of a Peruvian pisco-industry grape-pomace waste. At the same HPLE conditions (60% ethanol, 160◦C), the seed fraction extracts contained ~6 times more total polyphenol and presented ~5 times more antioxidant activity than the extract from the skin fraction. The lowest ethanol concentration (20%) and the highest temperature (160◦C) achieved the highest recovery of flavanols with 163.61 µg/g dw from seeds and 10.37 µg/g dw from skins. The recovery of phenolic acids was maximized at the highest ethanol concentration and temperature with 45.34 µg/g dw from seeds and 6.93 µg/g dw from skins. Flavonols were only recovered from the skin, maximized (17.53 µg/g dw) at 20% of ethanol and the highest temperature. The recovery of specific polyphenols is maximized at specific extraction conditions. These conditions are the same for seed and skin extractions. This alternative method can be used in other agroindustrial wastes in order to recover bioactive compounds with potential applications in the pharmaceutical and food industry.