The present study investigates the impact of solid-state fermentation on bee-collected pollen using a consortium of Lactobacillus plantarum, Apilactobacillus kunkeei, and Lactobacillus acidophilus. Another aim is to compare the nutritional and bioactive properties of natural versus fermented pollen, focusing on macronutrient composition, pH, acidity, lactic acid content, and profiles of polyphenolics and flavonoids. Our results indicated significant enhancements in the contents of amino acids, suggesting improved protein content, alongside increases in polyphenolic and flavonoid contents post-fermentation. According to the heat mapping and cluster analysis, increased antioxidant and antimicrobial activities against Gram-positive and Gram-negative bacteria, particularly E. coli, were observed in the fermented bee-collected pollen samples, which may have been due to the accumulation of phenolic compounds (e.g., ellagic acid, kaempferol, quercetin, and quercetin-3-O-rutinoside). Furthermore, significant positive correlations of the fermented bee-collected pollen samples with non-essential amino acids were recorded compared with the unfermented bee-collected pollen samples, which may have been due to the fermentation process and the conversion of proteins into free amino acids via proteolysis. Future research could explore the underlying mechanisms, the scalability of fermentation, its application in functional foods, and the health benefits of fermented bee-collected pollen in human diets.