The role of turbulence on two-stage ignition and subsequent flame stabilization at compression ignition engine conditions is assessed by performing direct numerical simulations in a simplified inflow-outflow premixed configuration. The thermochemical conditions are chosen to match those of the most reactive mixture in the Engine Combustion Network’s n-dodecane Spray A flame. Similar to previous work (Savard et al., Combust. Flame 208 (2019) 402–419) a transition of the stabilization mode from spontaneous ignition to deflagration is observed upon decreasing inflow velocity and/or increasing turbulent Reynolds number. However, for the present conditions there is a regime over which cool flames transition to deflagrations, while hot flames remain stabilized by spontaneous ignition, being pushed further away from the inlet. As cool flames transition to deflagrations, HTC ignition delay is increased considerably (up to 2.5 times larger). In addition, the flame structure in phase space is found to be strongly affected by the transition to deflagration, especially in cool flames. The mechanism controlling the transition, characterized by a reduction in displacement speed, differs between hot and cool flames: the former is attributed to an increase in progress variable gradients while the latter is attributed to a reduction in chemical source terms. The above trends are shown to correlate very well with a transition function and a similar functional dependence is found in laminar flames. Finally, a chemical explosive mode analysis provides further insight into the observed phenomena.