The strong link between atherosclerosis and luminal biomechanical stresses is well established. Yet, this understanding has not translated into preventative coronary diagnostic imaging, particularly due to the under-explored role of coronary anatomy and haemodynamics in plaque onset, which we aim to address with this work. The left coronary trees of 20 non-stenosed (%diameter stenosis [%DS] = 0), 12 moderately (0 < %DS < 70) and 7 severely (%DS ≥ 70) stenosed cases were dissected into bifurcating and non-bifurcating segments for whole-tree and segment-specific comparisons, correlating nine three-dimensional coronary anatomical features, topological shear variation index (TSVI) and luminal areas subject to low time-average endothelial shear stress (%LowTAESS), high oscillatory shear index (%HighOSI) and high relative residence time (%HighRRT). We found that TSVI is the only metric consistently differing between non-stenosed and stenosed cases across the whole tree, bifurcating and non-bifurcating segments ( p < 0.002, AUC = 0.876), whereas average curvature and %HighOSI differed only for the whole trees ( p < 0.024) and non-bifurcating segments ( p < 0.027), with AUC > 0.711. Coronary trees with moderate or severe stenoses differed only in %LowTAESS ( p = 0.009) and %HighRRT ( p = 0.012). This suggests TSVI, curvature and %HighOSI are potential factors driving plaque onset, with greater predictive performance than the previously recognized %LowTAESS and %HighRRT, which appears to play a role in plaque progression.