Interfaces between layers in 3D-printed elements produced by extrusion-based material deposition were investigated on both macro- and micro-scales. On the macro-scale, compression and bend tests were performed on two 3D-printable cement-based compositions (3PCs), namely C1 and C2. The influences of binder composition and time interval between layers on layer-interface strength were critically analyzed. In the context of additive manufacturing, the optimized composition C2, containing pozzolanic additives, exhibited mechanical performance superior to that of the mixture with Portland cement as the sole binder. In particular, Mixture C2 showed a less pronounced decrease in interface tensile strength. Even for time intervals between depositions of two layers as long as 1 day the loss in corresponding flexural strength was below 25%, as compared with C2 specimens tested in the perpendicular direction. In contrast, the decrease in flexural strength measured for C1 specimens amounted to over 90% for the same set of parameters. Higher porosity at the interfaces of the printed concrete layers was identified as the cause for the lower interface strengths of C1. Microscopic observations supported the findings of the macroscopic investigations. While a pronounced recovery (“self-healing”) of the porous, discontinuous interlayers was observed with increasing age for Mixture C2, in case of C1 the filling products grown in the porous interlayer were found to be non-strengthening.