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Agro-industrial sector in Indonesia produces significant amounts of nutrient-rich waste and wastewater, which pose environmental risks but also present opportunities for valorization within a circular bioeconomy. Microalgae provide a promising solution for transforming these wastewaters into valuable products such as biomass for bioenergy, biofertilizers, pigments, nutraceuticals, and animal feed, all while helping to remediate pollutants. This review synthesizes current knowledge on the use of major Indonesian agro-industrial effluents, specifically palm oil mill effluent (POME), byproducts from cassava and sugarcane, and soybean residues, as substrates for microalgal biomass production and cultivation. Furthermore, various cultivation strategies are summarized, including autotrophic, heterotrophic, and mixotrophic methods, as well as the use of open ponds, photobioreactors, and hybrid systems. These cultivation processes influence biomass yield, metabolite production, and nutrient removal. Reported studies indicate high removal efficiencies for organic loads, nitrogen, and phosphorus, along with considerable production of lipids, proteins, pigments, and biofuels. Yet, effluent pretreatment, concerns about heavy metal and pathogen contamination, high downstream processing costs, and biosafety issues remains as challenges. Nonetheless, the application of microalgal cultivation into Indonesia’s agro-industrial wastes treatment can provide the dual benefits of waste mitigation and resource recovery, helping to advance climate goals and promote rural development.