This study investigated the phenolic composition and antioxidant activities of aqueous infusions from wild-grown caper (Capparis spinosa L.) and sea fennel (Crithmum maritimum L.) from the Dalmatia region (Croatia) before and after their submission to an in vitro digestion process. HPLC/UV-vis-DAD/ESI-MS analysis of the caper infusion identified rutin, kaempferol 3-O-rutinoside, and isorhamnetin 3-O-rutinoside as dominant flavonoids in the matrix together with a series of cinnamoylquinic acid derivatives, whereas in the sea fennel aqueous infusion chlorogenic acid (5-caffeoylquinic acid), its isomers, and higher derivatives were identified as almost the sole class of phenolics. Both infusions exhibited good and dose-dependent antioxidant activity before in vitro digestion by the DPPH method, the β-carotene bleaching method, and copper-induced oxidation of human LDL. The amount of total phenolics (Folin-Ciocalteu assay) strongly decreased in digested samples (from 3.0 and 2.2% in caper and sea fennel infusions, respectively, to <1.0%), as did their antioxidant activity as measured by the three aforesaid methods. The results showed that the majority of phenolic compounds detected in both infusions are not stable under applied simulated gastrointestinal conditions and that the stability of these secondary metabolites strongly depends on the nature of the corresponding matrix.