Accurate assays of plant antioxidants and other phytochemicals require efficient extraction conditions and enable rigorous assessments of crop varieties and production systems. This study assessed the extraction of phytochemicals and antioxidants from conventionally or organically grown red and golden beets (Beta vulgaris L.), using twenty solvent (S1eS20) mixtures containing water, methanol, and ethanol alone or with acids (ascorbic, formic, acetic). Red beetroot extracted with methanol with or without acid had the highest betanin content (2791.0 mg/g and 8222.3 mg/g of fresh weight [FW], respectively) and golden beetroot extracted with methanol/ascorbic acid/water had the highest vulgaxanthin I (193.7 mg/g and 15.0 mg/g of FW, respectively). The radical-scavenging activity and total phenolics in beetroot extracts reflected the different extraction efficiency of each solvent. UHPLC-QTOF-MS was used to identify twenty-seven phytochemicals, including 23 betalains, 2 amino acids, and 2 phenolic acids. Chemometric approaches discriminated the beet varieties and different extracts within one variety based on the composition and abundance of the key phytochemicals. The red beetroot extracted with aqueous ethanol with or without acid (S5, S7, S8, S9), and golden beetroot extracted with methanol-containing solvents (S15 for conventionally and S20 for organically) had the highest levels of phytochemicals, suggesting that these conditions efficiently extract key phytochemicals.