Swine wastewater is a nutrient-rich waste stream with considerable potential for cyanobacterial cultivation and resource recovery. However, its impacts on microbial community dynamics and antibiotic resistance genes (ARGs) remain poorly understood. This study evaluated the cultivation of Arthrospira platensis in a medium containing 25% swine wastewater and 75% Zarrouk medium (SWW₂₅) using a flat-panel photobioreactor. A. platensis achieved a biomass concentration of 1.58 ± 0.02 g/L, a biomass productivity of 0.11 ± 0.01 g/L/d, and a specific growth rate of 0.26 ± 0.01 d⁻¹. Simultaneously, the system removed 98.5% of ammonium nitrogen and 80% of orthophosphate. Metagenomic analysis indicated changes in bacterial community composition during A. platensis cultivation. Microbial community analysis revealed shifts in relative abundance after cultivation, likely associated with changes in community composition following Arthrospira biomass enrichment, while Proteobacteria, Firmicutes, and Synergistota remained among the dominant phyla. In addition, ARG profiling indicated a decline in ARG diversity and read counts during cultivation, whereas tet(X) remained the only detectable ARG after A. platensis cultivation. Collectively, these findings suggest that A. platensis cultivation under non-axenic conditions was associated with biomass production, nutrient removal, and changes in microbial community composition and ARG profiles in swine wastewater.