Feijoa (Acca sellowiana Berg) is an emerging Mediterranean crop valued for its nutraceutical potential but still underexplored with respect to cultivar and harvest stage. This study investigated two cultivars, ‘Mammoth’ and ‘Apollo’, harvested one week apart (4 and 11 November), to assess morphological traits, phenolic composition, antioxidant activity, vitamin C, and iodine. Fruit morphology, firmness, and basic quality indices (TSS, TA, pH, TSS/TA) were determined, while phenolic compounds were profiled by UHPLC–Q-Orbitrap HRMS. Antioxidant activity was measured by ABTS, DPPH, and FRAP assays; vitamin C by DCPIP titration; and iodine by iodometric analysis. ‘Apollo’ produced larger and firmer fruits, especially at the first harvest (105.6 g), while ‘Mammoth’ showed smaller and softer fruits. TSS remained stable (11 °Brix), whereas TA decreased and pH increased over time, raising the TSS/TA ratio and suggesting improved flavor balance at later harvests. Peel consistently contained higher bioactive levels than pulp, with catechin as the dominant phenolic compounds (up to 345 µg g−1 dw in ‘Apollo’ peel). Antioxidant activity was markedly higher in peel, with ‘Mammoth’ showing stronger early FRAP values and ‘Apollo’ increasing at the later harvest. Vitamin C and iodine were about threefold higher in peel than pulp and increased over time, reaching maxima in late-harvest peel samples. Overall, cultivar and harvest stage significantly influenced fruit quality and nutraceutical value. Peel, particularly that of late-harvested ‘Apollo’, represents a promising resource for functional foods and the valorization of processing by-products.