This study is targeted at agricultural waste-derived heterogeneous catalysts, which have been effectively employed for Biginelli reaction. The application of cotton waste (Gossypium) derived lignin as a heterogeneous catalyst for C–C bond formation via one pot multicomponent Biginelli reaction. Here we hypothesize that the preparation of bio-waste derived catalyst by high temperature pyrolysis method under anaerobic conditions. The bio-waste derived heterogeneous catalyst (BDC) was well characterized by using different analytical techniques such as BET, SEM, TEM, XRD, DSC, TGA, ICP. The acidity of the catalyst was determined by a Hammett indicator test and titration method. An excellent yield of 6-methyl-2-oxo/thio-4-phenyl substituted-1,2,3,4-tetrahydropyrimidine-5-ethyl carboxylate derivatives was obtained in shorter reaction time (>80% yield in 15–30 min). The catalyst used in these studies has the advantage of being a waste material. Consequently, it is a low-cost, easily prepared, recyclable and environmentally benign. In addition, the use of a biogenic renewable catalyst, its atom economy, and room temperature and solvent-free reaction conditions and the avoidance of column chromatography make the protocol highly significant from green and sustainable chemistry perspectives. The synthesized compounds were characterized by modern analytical techniques like NMR, MS, FT-IR, CHNS analysis. The experimental parameters like % mole of catalyst, mole ratio, temperature and time for reaction completion were also optimized to achieve maximum yield and purity. The surface interaction between BDC and reactant was also studied.