Rising concerns over environmental and health issues of internal combustion engines, along with growing energy demands, have motivated investigation into alternative fuels derived from biomasses, such as biodiesel. Investigating engine and exhaust emission behaviour of such alternative fuels is vital in order to assess suitability for further utilisation. Since many parameters are relevant, an effective multivariate analysis tool is required to identify the underlying factors that affect the engine performance and exhaust emissions. This study utilises principal component analysis (PCA) to present a comprehensive correlation of various engine performance and emission parameters in a compression ignition engine using diesel, biodiesel and triacetin. The results show that structure-borne acoustic emission is strongly correlated with engine parameters. Brake specific NOx, primary particle diameter and fringe length increases by increasing the rate of pressure rise. Longer ignition delay and higher engine speeds can increase the nucleation particle emissions. Higher air-fuel equivalence ratio can increase the oxidative potential of the soot by increasing fringe distance and tortuosity. The availability of oxygen in the cylinder, from the intake air or fuel, can increase soot aggregate compactness. Fuel oxygen content reduces particle mass and particle number in the accumulation mode; however, they increase the proportion of oxygenated organic species. PCA results for particle chemical and physical characteristics show that soot particles reactivity increases with fuel oxygen content.