Bee pollen is a nutrient-rich granule, but its hard cell wall limits the absorption of its nutrients by the human body. Fermenting bee pollen with lactic acid bacteria breaks down its cell wall and enhances its metabolite profile, improving nutrient availability. However, the differences in metabolites and cell wall disruption effects between mixed and single-strain fermentation have not been clarified. This study aimed to analyze the metabolites of Lactobacillus plantarum comprehensively fermented bee pollen (LPFP), Lactobacillus acidophilus fermented bee pollen (LAFP), and L. plantarum and L. acidophilus mixed fermented bee pollen (LMFP) using targeted and untargeted metabolomics as well as lipidomics, to explore the key metabolic pathways of LMFP. The results showed that under scanning electron microscopy (SEM), the cell wall of LMFP was more thoroughly disrupted. Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) and metabolic pathway enrichment analysis indicated that the degradation of flavonoids in LMFP was reduced, while the contents of total phenols, total flavonoids, rutin, and other polyphenols were significantly increased. Meanwhile, the metabolism of sucrose and amino acids in LMFP was enhanced, which might have contributed to the production of flavor compounds. Additionally, compared to LAFP and LPFP, triglycerides (TG) in LMFP increased by 8.14% and 9.85%, respectively, while the proportion of phosphatidylcholine (PC) decreased by 0.62% and 2.88%. Overall, this study presents a comprehensive metabolic profile of LAFP, LPFP, and LMFP, demonstrating how fermentation strategies affect cell wall disruption and metabolite diversity, laying a foundation for enhancing bee pollen's nutritional and functional properties.