The Colombian industrial sector is moving toward alternative forms of treatment of industrial waste, considering that the waste can be a source of raw material in the production chain. Thus, aiming at the decrease in mineral fertilizer use, and maintaining or even raising the crop yield, the sugarcane industry has recently advanced in the composting of the industrial waste and application in the field, both of them being potentially sustainable practices. This manuscript reports the economic benefits and the greenhouse gas (GHG) emissions related to the sugarcane production system in Colombia that has been simulated in this study to evaluate the beneficial effects of reusing industrial waste from ethanol production. This study was performed using the Virtual Sugarcane Biorefinery (VSB) modeling software for the simulation of agricultural and industrial parameters on integrated alternatives for the sugarcane industry. Colombian sugarcane sector was modeled using three scenarios representing agricultural systems that do not use composted industrial waste vs a paired scenario for each condition where composted waste is utilized. Regarding compost and vinasse use as fertilizer and soil conditioner, GHG emissions from the biogenic origin are not included as a reported item in the matrix of GHG emissions of the sugarcane sector. Inputs for the economic and environmental assessment models are based on actual operational data from two mill sites, one located in the traditional sugarcane production region of Cauca River Valley and the other one, on the agricultural expansion region of Llanos Orientales. Here, we have found that the reuse of composted industrial waste is beneficial and provides an economic cost savings of 2–6% per year. However, it also results in an annual increase of 10–20% in the GHG emissions.