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 (31P 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 (Tg) 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 Tg 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 Tg. 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.