Biofilms are structured microbial communities that underlie many chronic infections, including periodontal disease. Their resilience to antimicrobial treatments and immune responses presents major clinical challenges. Yet, the structural changes bacteria undergo during biofilm formation and the structural basis of cell-cell interactions within biofilms remain poorly defined. Treponema denticola, a key oral spirochete and periodontal pathogen, forms complex biofilms at disease sites in the oral cavity. Here, combining confocal laser scanning microscopy with fluorescence in situ hybridization (CLSM-FISH) and cryo-electron tomography (cryo-ET), we show that spiral-shaped planktonic cells undergo profound morphological transitions to form densely packed, intertwined cell-clusters often with distinct yarn- or braid-like architectures. Remarkably, we observed frequent lateral cell fusions within biofilms, suggesting a novel mechanism for maintaining homeostasis. Our cryo-ET data unraveled that T. denticola structurally remodels its periplasmic flagella during biofilm formation and maturation. Combining cryo-ET and sub-tomogram averaging, we resolved two distinct flagellar assemblies within biofilms at <9.0 Å. Further single particle analysis refined these to near-atomic resolution (<3.0 Å), resulting in complete atomic models of distinct flagellar conformations. In Td flagellum, we identified two previously uncharacterized proteins, conserved across the Treponema genus, which contribute to the complex asymmetric lattice comprising seven different components. Together, these findings uncovered novel architectural features of T. denticola biofilms and revealed how structural plasticity of the motility machinery facilitates stable community formation. This work highlights a previously unappreciated link between flagellar structure and biofilm development, potentially conserved across other pathogenic bacteria.