The present study assesses modifications to the fuel preparation process (and subsequent emissions impact) in a commercial diesel-fired gas turbine system for operation on soy biodiesel fuel (1399). The influence of liquid properties and injector operation on the resulting droplet sizes and evaporation characteristics are assessed. A theoretical analysis of plain-jet air blast atomization and subsequent spray properties at atmospheric and engine conditions is carried out for two plain-jet air blast atomizer configurations. An adaptation to an existing empirical Sauter mean diameter is presented that accounts for the differing fuel properties found in B99 compared to DF2. Detailed analysis of the liquid state on injection in terms of nondimensional analysis explains limitations observed in the adapted model. A theoretical analysis of the influence of the fuel injector operation and liquid properties on the fuel evaporation characteristics is also carried out. The results are related to previously, measured emissions performance. Finally, discussion of an alternative approach to improving performance is presented in which blends of ethanol and B99 are used to achieve fuel properties that result in further optimized fuel preparation and therefore potentially further improved emissions.