This chapter explores the complexities in halal certificationHalal certification of biomassBiomass-based food products. With rapid innovations in biotechnology and food processing, the emergence of biomass as a food ingredient introduces novel challenges for halal compliance. These challenges include the source of raw materialsMicrobial fermentation, microbial fermentationFermentation processes, enzymatic conversions, and the traceabilityTraceability of ingredients in the global supply chain. Comparative analysis of global halal standards from Indonesia, Malaysia, GCC countries, and Western certifiers reveals gaps and opportunities for harmonization. Case studies of microbial enzymes, dietary fibers, and fermentationFermentation-derived flavor enhancers are presented to demonstrate real-world issues. The chapter concludes with strategic recommendations to build an adaptive, science-based halal assurance systemHalal assurance system.