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Synthetic antioxidants in seafood face safety and sustainability concerns, prompting the search for natural alternatives. This study assessed polyphenol extracts from Sub-Saharan mangrove leaves (Avicennia marina and Rhizophora mucronata) as clean-label antioxidants for sea bream (Sparus aurata) fillets. Extracts obtained via ultrasound-assisted 70% ethanol extraction were rich in catechin (2.23 mg/mL), gallic, and ferulic acids (over 1.3 mg/mL), and contained natural BHT analogues, as profiled by HPLC-DAD and GC-MS. ORAC values reached 2.4–2.7 mmol TE/g. Fillets were treated with 0.2% extract by immersion and punctured alginate-encapsulated beads (10 g/100 g fish) and stored at 2 °C for 15 days. Encapsulated polyphenols were more effective than immersion, reducing peroxide value, TBARS, and TVB-N, and matching or exceeding synthetic BHT in preserving quality markers (pH, NADH, tryptophan, MIR PCA). Mangrove polyphenols, especially as encapsulated beads may provide a promising, sustainable alternative to synthetic seafood preservatives.