This study aimed to generate new functional ingredients from microalgae and wine pomace through starter-assisted fermentation. Five lactic acid bacteria (LAB) and five yeasts were variously chosen for their species diversity, origin, and metabolic potential. During fermentation, the combination of Chlorella vulgaris and wine pomace overcame the limited growth observed in pomace substrate, with all LAB and yeasts effectively utilizing sugars and synthesizing microbial metabolites. Additionally, the synergistic interplay between the substrates, alongside the enzyme specificity of the starter cultures, improved the bioavailability of phenolic compounds, particularly flavanols, flavonols, and procyanidins, while simultaneously generating unique peptides in the formulated ingredients. In some cases, these metabolic changes were associated with enhanced antioxidant activity, improved protein digestibility, and overall protein quality. Our findings highlighted the potential of fermented mixed substrates as new functional ingredients, with promising health-promoting benefits and significant potential for applications in the food industry.