High strength steels are widely used for structural applications, where a combination of excellent strength and ductile-to-brittle transition (DBT) properties are required. However, such a combination of high strength and toughness can be deteriorated in the heat affected zone (HAZ) after welding. This work aims to develop a relationship between microstructure and cleavage fracture in the most brittle areas of welded S690 high strength structures: coarse-grained and intercritically reheated coarse-grained HAZ (CGHAZ and ICCGHAZ). Gleeble thermal simulations were performed to generate three microstructures: CGHAZ and ICCGHAZ at 750 and 800 °C intercritical peak temperatures. Their microstructures were characterised, and the tensile and fracture properties were investigated at − 40 °C, where cleavage is dominant. Results show that despite the larger area fraction of martensite-austenite (M-A) constituents in ICCGHAZ 750 °C, the CGHAZ is the zone with the lowest fracture toughness. Although M-A constituents are responsible for triggering fracture, their small size (less than 1 μm) results in local stress that is insufficient for fracture. Crack propagation is found to be the crucial fracture step. Consequently, the harder auto-tempered matrix of CGHAZ leads to the lowest fracture toughness. The main crack propagates transgranularly, along {100} and {110} planes, and neither the necklace structure at prior austenite grain boundaries of ICCGHAZs nor M-A constituents are observed as preferential sites for crack growth. The fracture profile shows that prior austenite grain boundaries and other high-angle grain boundaries (e.g., packet and block) with different neighbouring Bain axes can effectively divert the cleavage crack. Moreover, M − A constituents with internal sub-structures, which have high kernel average misorientation and high-angle boundaries, are observed to deflect and arrest the secondary cracks. As a result, multiple pop-ins in load-displacement curves during bending tests are observed for the investigated HAZs.