The accumulation of pith in a coconut husk processing facility leads to disposal problems, fire hazards, and contamination of groundwater. The leachate contains phenolic compounds that percolate through the soil and contaminate groundwater. Monolignols (guaiacyl (G), syringyl (S), and p-hydroxyphenyl (H)) in soil and groundwater pose a threat to the land and water resources. This study focuses on minimizing waste accumulation by treating the accumulated pith with sodium hydroxide to recover lignin and sugar. Pith, which has about with 24% cellulose and 49% lignin, was used as a substrate for recovery of Kraft lignin (KL) and sugar. The operating condition for the recovery of KL was optimized using response surface methodology (RSM). Maximum KL recovery (~ 86%) was achieved with optimal biomass loading of 65 mg/ml, NaOH concentration 5.12% w/w, residence time 31 min, and temperature 121 °C. A glucose yield of 95% was obtained after 48 h of saccharification. The removal of the aromatic layer increased the crystallinity index (CrI) after hydrolysis from 65 to 81.7%. The S/G ratio of 0.49 indicated that the lignin structure of pith is a matrix with many branches, thus making the lignin matrix strong and rigid. [Figure not available: see fulltext.] © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.