The evolution of lignin, five- and six-carbon sugars, and other decomposition products derived from hemicelluloses and cellulose was monitored in a sulfite pulp mill. The wastewater streams were characterized and the mass balances throughout digestion and total chlorine free bleaching stages were determined. Summative analysis in conjunction with pulp parameters highlights some process guidelines and valorization alternatives towards the transformation of the traditional factory into a lignocellulosic biorefinery. The results showed a good separation of cellulose (99.64%) during wood digestion, with 87.23% of hemicellulose and 98.47% lignin dissolved into the waste streams. The following steps should be carried out to increase the sugar content into the waste streams: (i) optimization of the digestion conditions increasing hemicellulose depolymerization; (ii) improvement of the ozonation and peroxide bleaching stages, avoiding deconstruction of the cellulose chains but maintaining impurity removal; (iii) fractionation of the waste water streams, separating sugars from the rest of toxic inhibitors for 2nd generation biofuel production. A total of 0.173 L of second-generation ethanol can be obtained in the spent liquor per gram of dry wood. The proposed methodology can be usefully incorporated into other related industrial sectors.