The aviation industry is increasingly focused on the development of sustainable alternative fuels to augment and diversify fuel supplies while simultaneously reducing its environmental impact. The impact of airport operations on local air quality and aviation-related greenhouse gas emissions on a life cycle basis have been shown to be reduced with the use of alternative fuels. However, the evaluation of incremental variations in fuel composition of a single alternative fuel on the production of non-volatile particulate matter (nvPM) emissions has not been explored. This is critical to understanding the emission profile for aircraft engines burning alternative fuels and the impact of emissions on local air quality and climate change. A systematic evaluation of nvPM emissions from a GTCP85 aircraft auxiliary power unit (APU) burning 16 different blends of used cooking oil (UCO)-derived hydroprocessed esters and fatty acids (HEFA)-type alternative fuel with a conventional Jet A-1 baseline fuel was performed. The nvPM number- and mass-based emission indices for the 16 fuel blends and neat UCOHEFA fuel were compared against those for the baseline Jet A-1 fuel at three APU operating conditions. The large data set from this study allows for the correlation between fuel composition and nvPM production to be expressed with greater confidence. The reductions in nvPM were found to be greater with increasing fuel hydrogen content (higher proportion of UCO-HEFA in the fuel blend). For a 50:50 blend of UCOHEFA and Jet A-1, which would meet current ASTM specifications, the average reduction in nvPM number-based emissions was similar to 35%, while that for mass-based emissions was similar to 60%. The nvPM size distributions were found to narrow and shift to smaller sizes as the UCOHEFA component of the fuel blend increased. This shift has a greater impact on the reduction in nvPM mass compared to the overall decrease in the nvPM number when comparing the UCO-HEFA fuel blends to the baseline Jet A-1.