Fatigue cracks initiating from surface and sub-surface non-metallic inclusions (NMIs) have recently been demonstrated to be a necessary but not sufficient explanation for atypically short low-cycle fatigue life in Inconel 718 alloy at intermediate temperature. Therefore, the early stages of short crack propagation from surface NMIs were investigated in a crystallographic and two-dimensional versus three-dimensional morphological manner after room temperature low cycle fatigue (LCF) testing. In the present investigation, NMIs were purposely pre-cracked using different techniques to suppress the natural crack initiation period and thus the incubation period prior to the early stages of crack propagation. Under such fatigue testing conditions, different mechanisms of crack transmission from pre-cracked NMIs were identified: (i) no propagation, (ii) NMI/adjacent metallic grain interfacial debonding, (iii) transgranular crack propagation within the adjacent metallic grain. Focused-ion-beam cross-section observations of numerous fatigue tested NMIs aimed to define a morphological criterion for non-propagating NMIs. Large cracked NMIs at the surface (2c) with limited extension into the depth (a) did not propagate under such fatigue conditions for 2c/a ratio higher than 3. Furthermore, specific crystallographic relationships between NMIs and the adjacent metallic grain explained different crack propagation configurations from pre-cracked NMIs, i.e. interfacial debonding and transgranular crack propagation involving single or multiple-slip activity.