In Europe, diesel combustion is being banned due to the NOx and PM2.5 emissions impact on air quality. The bus sector is being electrified and is increasing its use of alternative fuels, such as natural gas (in spark ignition engines) and bioethanol (in compression ignition engines), to reduce such harmful emissions. Even if a diesel bus is equipped with selective catalytic reduction (SCR), its NOx emissions are reduced its but produces more NH3 emissions that are PM2.5 precursors. In developing countries, the air quality is still barely monitored, however, the air quality issue is well known and is being addressed. Moreover, the Ecuadorian sugar cane industry is seeking ways to increase its ethanol production. This is the ideal framework to explore a new technology and energy source in developing economies such as Ecuador. This paper explores the impact of the Ecuadorian diesel bus fleet conversion to hybrid compression ignition ethanol (HEV-ED95), hybrid diesel and plug-in hybrid flex-fuel using electricity and internal combustion engine ICE-E20 and ICE-E100. The impacts are measured in terms of final energy consumption, criteria pollutant emissions (NH3, NOx, PM2.5) and 100 years global warming potential in a well-to-wheels framework. For the tank-to-wheels data the method follows the typical values of conversion efficiency from final to useful energy (cross checked with a microsimulation model), the Tier 2 European Environmental Agency approach combined with ethanol influence on compression ratio, lower heating value, criteria emissions taken from a literature review, and well-to-tank emission factors for electricity (10−58% thermal natural gas or coal powerplant contribution), for ethanol from banana industry wastes (ED95, E20 and E100), gasoline and diesel from US databases. A discussion on whether sugarcane biorefineries are necessary is highlighted in the results. All input parameters have an uncertainty range between a minimum and a maximum and the probability for each is giving by a uniform distribution.