The correlation between lignin structure, its properties, and performance is crucial for lignin engineering in high-value products. Currently, a widespread approach is to compare lignins which differ by more than one parameter (i.e., Kraft vs organosolv vs lignosulfonates) in various applications by attributing the changes in their properties/performance specifically to a certain variable (i.e., phenolic −OH groups). Herein, we suggest a novel approach to overcome this issue by changing only one variable at a time while keeping all others constant before investigating the lignin properties/performance. Indulin AT (Ind-AT), a softwood Kraft lignin, was chosen as the model substrate for this study. Selective (analytical) lignin modifications were used to mask/convert specific functionalities, such as aliphatic (AliphOH) including benzylic −OH (BenzOH) and phenolic −OH (PhOH) groups, carboxyl groups (−COOH) and carbonyl groups (CO) via methylation, acetylation, and reduction. The selectivity and completeness of the reactions were verified by comprehensive NMR analysis ( 31 P and 2D HSQC) of the modified preparations together with state-of-the-art molar mass (MM) characterization. Methylene blue (MB) adsorption, antioxidant activity, and glass transition temperature (T g ) were used to demonstrate and compare the properties/performance of the obtained modified lignins. We found that the contribution of different functionalities in the adsorption of MB follows the trend BenzOH > −COOH > AlipOH > PhOH. Noteworthy, benzylic −OH contributes ca. 3 and 2.3 times more than phenolic and aliphatic −OH, respectively. An 11% and 17% increase of T g was observed with respect to the unmodified Indulin by methylating benzylic −OH groups and through reduction, respectively, while full acetylation/methylation of aliphatic and phenolic −OH groups resulted in lower T g . nRSI experiments revealed that phenolic −OH play a crucial role in increasing the antioxidant activity of lignin, while both aliphatic −OH groups and −COOHs possess a detrimental effect, most likely due to H-bonding. Overall, for the first time, we provide here a reliable approach for the engineering of lignin-based products in high value applications by disclosing the role of specific lignin functionalities.