Sepals and petals form the peels of pineapple fruits, which influence the size of cavities below the surface of the fruits (so-called “fruit eye”) and subsequently the fruit quality and edible rate. In this study, to investigate the underlying mechanisms controlling septal-petal formation in pineapple, we utilized a mutant of variety ‘Yulinglong’ with petaloid sepals for comparative analyses with the wild type. Phenotypic and microscopic observations confirmed the either partially or completely petalized structure of the sepals of the mutant. Comparative gene expression analysis identified two MADS-box family members AcPI and AcAP3 that are potentially associated with the petaloid sepals. Heterologous overexpression experiments in Arabidopsis and tobacco validated their functions in controlling the identity and organogenesis of sepals/petals, as well as confirmed their role in transforming sepals to petals. Protein—protein interaction experiments and gene expression profiling suggested that AcPI and AcAP3 may coordinately determine floral organogenesis in pineapple flower bud primordia differentiation. The results provide important insights into the molecular regulation of floral organ identity and peel structure formation in pineapple, which may be harnessed to improve fruit quality and edible rate for pineapple.