Nutrient recycling from biowaste is one of the sustainable approaches to managing waste. The aquaponic system is one of the nutrient recycling methods that can reduce water consumption and reuse the nutrient available in its ecosystem. The nutrient to fertilize the plant in aquaponic depends on the activities of microbes to convert the waste into the nutrient. To enhance the growth of the plants, some aquaponics systems still rely on chemical fertilizers. Kappaphycus alvarezii is one of the red seaweeds abundantly found in East Malaysia. After numerous processes such as carrageenan extraction, the biowaste derived from K. alvarezii still contains a nutrient that can be recycled. The present study explores the potential of K. alvarezii solid waste as fertilizer to grow Ocimum basilicum in an aquaponics system. In this study, the macro- and micronutrients in K. alvarezii solid waste were determined, and the prevalence of microbes in the aquaponics system was monitored using inductively coupled plasma-optical emission spectrometer (ICP-OES) and 16S metagenomic sequencing method, respectively. Based on the findings, the growth of O. basilicum supplemented with K. alvarezii biofertilizer was significantly higher than the negative control. For genetic expression study in O. basilicum, cinnamyl alcohol dehydrogenase (CAD), phenylalanine ammonia-lyase (PAL), and cytochrome p450 reductase (CPR) genes were upregulated. The O. basilicum is free from mycotoxin and heavy metals. Since K. alvarezii solid waste is rich with macro- and micronutrients, which are essential for plant growth and can enhance the growth of O. basilicum, K. alvarezii solid waste produced from bioethanol production could be a potential fertilizer.