The bridging defects compromise the structural integrity and strength of 3D-printed polymer parts with the Fused Filament Fabrication (FFF) process. Conventional approaches to avoid bridging defects include simply minimising bridging span and/or adding support structures, which greatly limit the freedom and flexibility of designing FFF-printed polymer products. To lift this limit, this study develops a systematic analytical–experimental framework to investigate the formation and evolution of bridging defects in Polylactic Acid (PLA) bridging beam structures printed using FFF and proposes mitigation methods by adjusting FFF print settings and optimising the beam structures’ geometries. The developed analytical models can capture temperature and elastic modulus evolution, as well as strand curvature, where the modelling results show good agreement with experimental measurements, with coefficients of determination, $R^2$, of up to 0.9433. Buckling behaviours are also modelled and quantified in terms of girder width, which increases from 1.2 mm to 4.3 mm as the span length increases from 60 mm to 140 mm, respectively. The obtained results indicate that thermally induced residual stress plays a dominant role in triggering structural instability in support-free beam structures, where the gravitational contribution was found to be comparatively small. Key FFF printing factors influencing bridging defects are also identified for practical guidance of defect mitigation.