Treponema denticola is a Gram-negative, motile oral spirochete implicated in periodontal diseases through the formation of biofilms. These structured microbial communities promote chronic infections by conferring resilience to antibiotics and host defenses, yet the structural adaptations underpinning their assembly remain poorly defined. Using an integrated, cross-scale approach combining confocal laser scanning microscopy with fluorescence in situ hybridization, cryo-electron tomography, single particle cryo-electron microscopy and phylogenomics, we reveal that T. denticola undergoes striking morphological transitions during biofilm formation. We found that the structural remodelling of periplasmic flagella underpins this process and resolved two distinct flagellar conformations at sub-3 Å resolution. Our analysis revealed unexpected complexity within planktonic flagella, which comprise seven different proteins, including four previously uncharacterized components. The complex asymmetric assembly is the first complete model of a periplasmic flagellum and uncovers mechanisms for curvature generation within the characteristic spiral filaments. In contrast, within biofilms we observe remodelling to only core flagellins and demonstrate their crucial role in mediating cell–cell contacts within biofilm. These findings reveal multi-scale structural and functional adaptations linking flagellar remodelling to stable biofilm architecture with broad implications across diverse bacterial pathogens.