Research on lignin valorization has gained ground, driven by its potential to replace fossil-based phenolics in bio-based applications. Technical lignins are structurally complex and still poorly characterized, prompting the need for novel extraction processes for lignin of high analytical quality. In this context, a two-step cyclic extraction process for lignin was contrasted with a one-step cyclic extraction. The latter was shown to preserve the native structure of the spruce lignin product better and improved the yields of both the extracted lignin and residual fiber fraction. The application of the one-step cyclic extraction process to birchwood resulted in a similar protection of the lignin structure. Overall, a flexible physical protection (FPP) process for extraction of lignin with an abundance of native bonds is presented. The lignin product has a high abundance of ether bonds and hydroxyl functionalities, which are of interest in biochemical, polymer, and material applications.