For structural assessment and optimal design of thick-section high-strength steels in applications under harsh service conditions, it is essential to understand the cleavage fracture micromechanisms. In this study, we assess the effects of through-thickness microstructure of an 80-mm-thick quenched and tempered S690 high-strength steel, notch orientation, and crack tip constraint in cleavage nucleation and propagation via sub-sized crack tip opening displacement (CTOD) testing at −100 °C. The notch was placed parallel and perpendicular to the rolling direction, and the crack tip constraint was analysed by varying the a/W ratio: 0.5, 0.25, and 0.1. The notch orientation does not play a role, and the material is considered isotropic in-plane. Nb-rich inclusions were observed to act as the weak microstructural link in the steel, triggering fracture in specimens with the lowest CTOD values. While shallow-cracked specimens from the top section present larger critical CTOD values than deep-cracked ones due to stress relief ahead of the crack tip, the constraint does not have a significant influence in the middle due to the very detrimental microstructure in the presence of Nb-rich inclusions. Some specimens show areas of intergranular fracture due to the combined effect of C, Cr, Mn, Ni, and P segregation along with precipitation of Nb-rich inclusions clusters on the grain boundaries. Several crack deflections at high-angle grain boundaries were observed where the neighbouring sub-structure has different Bain axes.