Abstract: To improve the quality of processed blue honeysuckle (Lonicera caerulea L.) products, this study employed a mixed starter culture of lactic acid bacteria (Lactobacillus acidophilus, Lactobacillus fermentum, and Lacticaseibacillus rhamnosus) in combination with eggshell powder for co-fermentation to produce calcium-enriched fermented blue honeysuckle juice. An unfermented group, a single lactic acid bacteria fermentation group, and co-fermentation groups with lactic acid bacteria and eggshell powder (at addition levels of 0.5% and 1%) were established to systematically evaluate juice yield, soluble solids contents, sensory quality, calcium contents, polyphenol and anthocyanin contents, as well as the composition of non-volatile metabolites. The results showed that lactic acid bacteria fermentation increased the soluble solids contents of the juice, reduced bitterness and astringency, and promoted the accumulation of total phenolics and anthocyanins. Co-fermentation with eggshell powder effectively increased the bioavailable calcium contents of the juice and promoted the conversion of calcium carbonate into readily absorbable calcium chelates. Among them, the 1% eggshell powder group exhibited total calcium, organic acid-bound calcium, and protein-bound calcium contents of 2229.73, 1681.44, and 537.90 mg/L, respectively. A total of 732 metabolites were identified by liquid chromatography–mass spectrometry. Lactic acid bacteria fermentation effectively promoted the enrichment of functional components such as flavonoids, phenolic acids, terpenoids, glycosides, alkaloids, and amino acid derivatives, with the co-fermentation groups supplemented with eggshell powder showing the most pronounced effects. In conclusion, the synergistic fermentation of lactic acid bacteria and eggshell powder significantly improved the flavor and nutritional quality of blue honeysuckle juice, providing a new strategy for the development of calcium-enriched functional beverages and the high-value utilization of blue honeysuckle resources.