Incessant demand for fossil derived energy and the resulting environmental impact has urged the renewable energy sector to conceive one of the most anticipated sustainable, alternative “drop-in” fuels for jet engines, called as, Bio-Synthetic Paraffinic Kerosene (Bio-SPKs). Second (Camelina SPK & Jatropha SPK and third generation (Microalgae SPK) advanced biofuels have been chosen to analyse their influence on the behaviour of a jet engine through numerical modelling and simulation procedures. The thermodynamic influence of each of the biofuels on the gas turbine performance extended to aircraft performance over a user-defined trajectory (with chosen engine/airframe configuration) have been reported in this paper. Initially, the behaviour of twin-shaft turbofan engine operated with 100% Bio-SPKs at varying operating conditions. This evaluation is conducted from the underpinning phase of adopting the chemical composition of Bio-SPKs towards an elaborate and careful prediction of fluid thermodynamics properties (FTPs). The engine performance was primarily estimated in terms of fuel consumption which steers the fiscal and environmental scenarios in civil aviation. Alternative fuel combustion was virtually simulated through stirred-reactor approach using a validated combustor model. The system-level emissions (CO 2 and NOx) have been numerically quantified and reported as follows: the modelled aircraft operating with Bio-SPKs exhibited fuel economy (mission fuel burn) by an avg. of 2.4% relative to that of baseline (Jet Kerosene). LTO-NOx for the user-defined trajectory decreased by 7–7.8% and by 15–18% considering the entire mission. Additionally, this study reasonably qualitatively explores the benefits and issues associated with Bio-SPKs.