Microstructure formation in individual layers during fused filament fabrication (FFF) of Pi-shaped multilayer single-walled polymer sample was studied by simultaneous measurement of small- and wide-angle X-ray scattering (SAXS and WAXS, respectively) methods employing synchrotron radiation. We investigated individual layers and the welding zone between individual layers. As a model material, we used isotactic polypropylene (iPP), which is a commodity semicrystalline polymer and has a strong potential as a feedstock material for additive manufacturing. The layers were deposited by an FFF three-dimensional (3D) printer that was custom-built to fit into the synchrotron beamline. WAXS data were utilized to determine the temperature of the irradiated volume. The polymer microstructure was characterized in terms of crystallinity and long-spacing. Avrami analysis indicates that the crystallization behavior of iPP in thin layers is rather similar to that observed in quiescent crystallization of bulk iPP, suggesting similar nucleation and growth mechanisms. Our results revealed a variation of crystallinity across the individual layers, reflecting the influence of interfaces (free surface and welding zone) on the final crystallinity of the thin layer (thickness h = 0.02 cm): the polymer is more crystalline in the bulk of the layer and less crystalline in the vicinity of the interfaces. This effect can be advantageous to facilitate the welding between the layers, i.e., to improve the overall mechanical performance of the 3D-printed object because welding between layers is expected to occur by polymer chain interdiffusion. Along the thin layer we observed a higher crystallinity near the corners attributed to a deceleration of the print head.