Quinoa is widely noted for its nutritional value. The seed is the main edible part of the plant and exists in at least three different colors: white, red and black. This study utilized a pressurized hot water extraction (PHWE) for the extraction of phytochemicals from quinoa. Chemical fingerprints with LC/UV and LC/MS using a targeted approach and pattern recognition tools were used to evaluate the quinoa extracts. The antioxidant properties for various types of quinoa were evaluated using DPPH assay, ABTS assay and the cytoprotective effect of quinoa extracts were investigated in HMEC-1 cell line. Distinctive chemical profiles obtained from black and red quinoa were well correlated with the antioxidant activities and cytoprotective effects. The combination of PHWE, chemical standardization with LC/UV and LC/MS, pattern recognition tools and biological assay provided an approach for the evaluation and eventual production of quinoa extracts for functional food.