This study investigates combustion and emission characteristics of a contemporary single-cylinder compression ignition engine fuelled with diesel, fatty acid methyl esters (FAME) and hydrotreated vegetable oil (HVO). These two drop-in fuels have an increasing share in automotive supply chains, yet have substantially different physical and auto-ignition properties. HVO has a lower viscosity and higher cetane number, and FAME has contrary characteristics. These parameters heavily affect mixture formation and the following combustion process, causing that the engine pre-optimized to one fuel option can provide deteriorated performance and excess emissions if another sustainable option is applied. To investigate the scale of this problem, injection pressure sweeps were performed around the stock, low NOX and low PM engine calibration utilizing split fuel injection. The results showed that FAME and HVO prefer lower injection pressures than diesel fuel, with the benefits of simultaneous reduction of all emission indicators compared to DF. Additionally, reduction of injection pressure from 80 MPa to 60 MPa for biodiesels at low engine load resulted in improved brake thermal efficiency by 1 percentage point, due to reduced parasitic losses in the common rail system.