For this purpose, lignin was extracted from cotton stalk via both classical and modified version of Zilliox & Debeire method (1998) and extracted lignins were characterized by means of their antimicrobial activity against E. coli and Bacillus pumilus in both liquid and solid medium. Additionally, garlic juice extracted from green garlic stalk and olive mill wastewater were also characterized in the same way. Fragmentation processes such as ultrasonication and TiO2-assisted photocatalytic oxidation were utilized to isolate lignin fragments that demonstrate antimicrobial activity and the antimicrobial effects of post-treated lignin samples were evaluated against tested bacteria. Following these steps, xylan-based biodegradable films containing compounds that demonstrate antimicrobial activity were characterized against B. pumilus & E. coli by means of their antimicrobial properties. Moreover, lignin based compounds having antimicrobial activity were characterized by means of their chemical structure via FTIR and LC/MS analysis.