The Integrated Fixed-film Activated Sludge (IFAS) partial nitritation/anammox (PN/A) process offers robust nitrogen removal, yet startup using pre-colonized carriers incurs high logistical costs. This study investigated the mechanism of inoculating a pilot-scale IFAS system with granular anammox sludge to treat anaerobic digestion supernatant. The treatment train integrated coagulation, pre-aeration, and an IFAS-PN/A unit. The granular-inoculated IFAS-PN/A unit achieved stable biofilm formation and a nitrogen removal rate of 0.36 kg N m⁻³ d⁻¹, benefiting from the effective interception of excessive organic carbon by the preceding coagulation and pre-aeration steps. Microbial analysis identified Candidatus brocadia as the dominant anammox genus, revealing a distinct migration pathway: bacteria transferred from disintegrating granules to the suspended sludge—acting as a transitional vector—before ultimately colonizing the carriers. While granular biomass diminished, anammox abundance in the biofilm increased to 12.0% by day 166. Furthermore, distinct spatial niches were observed: ammonium-oxidizing bacteria (AOB) dominated the suspended sludge, while nitrite-oxidizing bacteria (NOB) were effectively suppressed. These findings demonstrate the feasibility of granular inoculation for cost-effective IFAS startup and provide critical insights into the bacterial migration dynamics required for stable operation.