The study explores the potential of *Neurospora intermedia* in converting food and agricultural by-products into valuable foods through fungal fermentation. Using a multi-omics approach, the researchers characterized *oncom*, a traditional fermented food from Java, Indonesia, which is traditionally made from soy milk by-products. Metagenomic sequencing revealed that *N. intermedia* dominates *oncom* fermentation. Further transcriptomic, metabolomic, and phylogenomic analyses showed that *N. intermedia* degrades pectin and cellulose during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. The fungus grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and created foods that were positively perceived by consumers outside Indonesia. These findings highlight the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products, contributing to food sustainability and security.The study explores the potential of *Neurospora intermedia* in converting food and agricultural by-products into valuable foods through fungal fermentation. Using a multi-omics approach, the researchers characterized *oncom*, a traditional fermented food from Java, Indonesia, which is traditionally made from soy milk by-products. Metagenomic sequencing revealed that *N. intermedia* dominates *oncom* fermentation. Further transcriptomic, metabolomic, and phylogenomic analyses showed that *N. intermedia* degrades pectin and cellulose during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. The fungus grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and created foods that were positively perceived by consumers outside Indonesia. These findings highlight the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products, contributing to food sustainability and security.