Atrial fibrillation (AF) is a major cause of stroke and there has been much interest in the underlying mechanisms leading to this higher risk of thrombus formation. The latter risk correlates with four morphologies of the left atrial appendage (LAA), i.e. chicken wing (CW), broccoli (BR), cactus (CA) and windsock (WS). We present a mechanistic study of coagulation dynamics in blood flow in a series of 2D models of the left atrium (LA) to dissect the impact of LAA shape on thrombus formation. Interactions between blood flow, viscosity and key clotting proteins (thrombin, fibrinogen and fibrin) were modelled during 1 minute of pulsatile LA blood flow to simulate the blood gelification process leading to thrombus formation. Simulations were performed in sinus rhythm (SR) and AF by varying the active contraction of the LAA and pulmonary vein inflow velocities. In the CW morphology, fibrin inside the LAA was almost completely washed out after 28 seconds in SR, while in AF the gelification process was slow, suggesting the CW has the lowest risk of thrombus formation. Conversely, the BR morphology had the highest risk of thrombus formation due to a region of sustained flow stasis which prevented fibrin washout during SR and facilitated the shortest time to thrombus formation in AF.