The goal of this paper is to evaluate the supply of sugarcane to mills and also the supply of green harvesting residues to second-generation ethanol plants under three different strategies: chopping, baling and integral harvesting. A dynamic model was developed in order to simulate the biomass flow along the main activities within sugar-ethanol supply chain. Weather, geographical and operational constraints were considered for calculating the biomass availability. The model is able to quantify the production of sugar and first-generation ethanol from mills, electricity surplus from co-generation and second-generation ethanol with the aim of evaluating operational, economic and environmental indicators. In this study it was found that the integral harvesting is the best strategy for supply the residues in terms of cost (5.90 USD/dry t), energy inputs (56.89 MJ/dry t) and carbon emissions (4.18 kg CO2/dry t). The low resources utilization due to the inappropriate harvest-load-transport synchronization creates bottlenecks that decrease the system throughput, leaving the door open for further improvements