Anaerobic microalgae fermentation, leveraging its cost-effectiveness and the adaptability of mixed cultures, holds promise for carboxylate biosynthesis. Microalgae, with their abundant carbohydrates and proteins, stand out as an optimal substrate for this process among various options. Furthermore, microalgae fermentation not only shows the potential to mitigate risks associated with algae blooms but also aligns with the need for sustainable practices. However, the limited utilization rate of microalgae in anaerobic fermentation poses challenges to achieving high production rates of desired products. In this study, we implemented a bioaugmentation process with yeast to enhance carboxylate production performance of microalgae fermentation. The results demonstrated a fourfold increase in carboxylate yield with the addition of yeast. In-situ ethanol production facilitated the conversion of short-chain carboxylic acids into medium-chain carboxylates, achieving a yield of 46.3 mM-C/g VS. The presence of yeast significantly enhanced substrate utilization from 20 % to 80 %, steering the metabolic pathway towards chain elongation. Metagenomic analysis further revealed metabolic shifts following yeast addition, particularly an increased abundance of genes involved in acetyl-CoA production. Notably, the aldehyde:ferredoxin oxidoreductase (AOR) pathway emerged as a key driver in butanol production. These findings highlight the improved performance of anaerobic microalgae fermentation with yeast, enabling efficient production of higher value bioproducts while eliminating the need for external electron donors.