Lignin contains benzene rings, carbonyl groups, and phenolic groups that serve as natural macromolecular UV absorber. However, lignin provides insufficient protection in the UVA region because it lacks a long conjugated structure. In this study, we propose a flavonoids-in-lignin coextraction strategy to improve lignin’s UVA protection performance. Flavonoids-containing lignin was isolated from Musa basjoo ( Musa basjoo Siebold ) and Moso bamboo ( Phyllostachys edulis ) leaves using l -cysteine ( l -cys)-assisted extraction, and the contents of flavonoids in lignin could be further enhanced by employing non-dewaxed sources. Lignin’s UV-protective performance and antioxidant activity were improved as more flavonoids were reserved. Particularly, lignin isolated from non-dewaxed bamboo leaves (NBL) exhibited the best UV protection performance, achieving a sun protection factor (SPF) value of 40.99 with the addition of 5 wt % lignin into SPF 15 commercial sunscreen, representing a 143% enhancement, and a UVA protection factor (PFA) value of 12.17, reflecting a 109% increment. The sunscreens prepared from flavonoid-rich lignin maintained SPF values exceeding 30 and PFA values exceeding 9 (PA+++) even after 8 h of UV irradiation, indicating their long-term UV-protective properties. Furthermore, flavonoids-in-lignin coextraction demonstrated superior UV-protective performance compared to alkali lignin with adscititious flavonoid extracts. This study leverages the inherent advantages of natural plant cell wall components through a straightforward coextraction strategy, further unlocking the potential of lignin for sunscreen applications.