The aviation sector has begun to adopt alternative fuels in an effort to reduce net greenhouse gas (GHG) emissions and reduce their impact on climate change. While many lab and flight-based studies have been completed for hydro-treated esters and fatty acids (HEFA) and Fischer-Tropsch (FT) alternative fuels, only one lab study has been conducted on alcohol-to-jet synthetic paraffinic kerosene (ATJ-SPK) fuels. Here we report results from the Civil Aviation Alternate Fuels Contrails and Emissions with high blend Biojet (CAAFCEB) project which was conducted in order to gather in-flight emissions data and compare an ethanol-based ATJ-SPK fuel blend and conventional JP-5 fuel to conventional Jet A1 fuel. A research aircraft was flown while fueled with the different fuels and in-flight cruise measurements were made by a second research aircraft gathering emissions and contrail data. In this study we report particle number emission index ratios with effective cutoff diameters of 15 and 7.7 nm for total particles and 13 nm for nonvolatile particles for GE CF700-2D2 engines at cruise. The ATJ-SPK blend was found to significantly reduce total and nonvolatile particle number emissions by up to 97% compared to Jet A1 fuel, likely due to the much lower aromatic and sulfur content and higher hydrogen content of the fuel. On the other hand, the total particle emissions for the JP-5 were found to have been 4% smaller than for Jet A1; this small difference is likely due to the similar fuel compositions.