Caffeoylquinic acids are some of the chemophenetically significant specialized metabolites found in plants of the family Asteraceae Dumort., possessing a broad spectrum of biological activities. As they might be potential mitochondria-targeted antioxidants, effective preparation methods-including extraction, isolation, and purification of caffeoylquinic acids from plant sources-are in great demand. The aim of this study was to fractionate the caffeoylquinic acids from cultivated wormwood (Artemisia absinthium L.) and silver wormwood (Artemisia ludoviciana Nutt.) herb acetone extracts and evaluate their phytochemical profiles, antioxidant activity (radical scavenging and reducing activities), effects on kidney mitochondrial functions, and cytochrome-c-reducing properties. The main findings of our study are as follows: (1) Aqueous fractions purified from wormwood and silver wormwood herb acetone extracts are rich in monocaffeoylquinic acids (chlorogenic acid, neochlorogenic acid, 4-O-caffeoylquinic acid), while methanolic fractions purified from wormwood and silver wormwood herb acetone extracts are rich in dicaffeoylquinic acids (4,5-dicaffeoylquinic acid, 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid). Aqueous fractions purified from wormwood and silver wormwood herb acetone extracts were solely composed of monocaffeoylquinic acids. Methanolic fractions purified from wormwood and silver wormwood herb acetone extracts contained only dicaffeoylquinic acids. (2) Fractions purified from silver wormwood herb acetone extracts stood out as having the greatest content of caffeoylquinic acids. (3) The greatest radical scavenging activity was determined in the dicaffeoylquinic-acid-rich fraction purified from silver wormwood herb acetone extract; the greatest reducing activity was determined in the dicaffeoylquinic-acid-rich fraction purified from wormwood herb acetone extract. (4) The effect of both fractions on mitochondrial functions was dose-dependent; lower concentrations of caffeoylquinic-acid-rich fractions had no effect on mitochondrial functions, whereas higher concentrations of caffeoylquinic-acid-rich fractions reduced the state 3 respiration rate (with the complex-I-dependent substrate glutamate/malate). (5) Both monocaffeoylquinic- and dicaffeoylquinic-acid-rich fractions possessed cytochrome-c-reducing properties; the greatest cytochrome c reduction properties were determined in the dicaffeoylquinic-acid-rich fraction purified from wormwood herb acetone extract. In summary, these findings show that caffeoylquinic acids might be beneficial as promising antioxidant and cytochrome-c-reducing agents for the modulation of mitochondria and treatment of various mitochondrial-pathway-associated pathologies.