The content of carotenoids, chlorophylls, phenolics, and tocols in pistachios ( Pistacia vera L.) has not been methodically quantified. The objective of this study was to first optimize extraction protocols for lipophilic nutrients and then quantify the content of two phenolic acids, nine flavonoids, four carotenoids, two chlorophylls, and three tocols in the skin, nutmeat, and whole nut of California pistachios. The dominant bioactives in whole pistachios are lutein [42.35 μg/g fresh weight (FW)], chlorophyll a (142.24 μg/g FW), γ-tocopherol (182.20 μg/g FW), flavan-3-ols (catechins) (199.18 μg/g FW), luteolin (217.89 μg/g FW), myricetin (135.18 μg/g FW), and cyanidin-3-galactose (38.34 μg/g FW) in each nutrient class. Most phenolics are present in the skin, while the lipophilic nutrients are dominantly present in the nutmeat. Digestion with a gastrointestinal mimic showed <10% of most hydrophilic compounds are released from pistachio matrices. In conclusion, 9 lipophilic and 11 hydrophilic bioactives in pistachios are systematically quantified.