Aortic valve replacement has become an increasing concern due to the rising prevalence of aortic stenosis in an ageing population. Existing replacement options have limitations, necessitating the development of improved prosthetic aortic valves. In this study, flow characteristics during systole in a stenotic aortic valve case are compared with those downstream of two newly designed surgical bioprosthetic aortic valves (BioAVs). To do so, advanced three-dimensional fluid–structure interaction simulations are conducted and dedicated analysis methods to investigate jet flow configuration and vortex dynamics are developed. Our findings reveal that the stenotic case maintains a high jet flow eccentricity due to a fixed orifice geometry, resulting in flow separation and increased vortex stretching and tilting in the commissural low-flow regions. One BioAV design introduces non-axisymmetric leaflet motion, which reduces the maximum jet velocity and forms more vortical structures. The other BioAV design produces a fixed symmetric triangular jet shape due to non-moving leaflets and exhibits favourable vorticity attenuation, revealed by negative temporally and spatially averaged projected vortex stretching values, and significantly reduced drag. Therefore, this study highlights the benefits of custom-designed aortic valves in the context of their replacement through comprehensive and novel flow analyses. The results emphasise the importance of analysing jet flow, vortical structures, momentum balance and vorticity transport for thoroughly evaluating aortic valve performance.