Biomass biomanufacturing represents a sustainable alternative to fossil-based production systems by utilizing renewable feedstocks to generate value-added chemicals and biofuels. However, the widespread industrial application of these processes faces two primary challenges: the reoxidation of target products and carbon efficiency losses. Reoxidation, both biotic and abiotic, leads to the conversion of desirable end-products back into carbon dioxide, significantly diminishing yield and economic feasibility. These losses are exacerbated under aerobic fermentation conditions and during downstream processing. Additionally, the metabolic imbalance and redox stress during microbial conversions further limit the carbon-to-product efficiency. While heteroatom-containing molecules are thermodynamically prone to reoxidation, attempts to bypass this through synthetic biology and metabolic engineering are yet to achieve complete carbon retention. This chapter reviews the fundamental mechanisms of reoxidation, key chemical and biological pathways responsible for product degradation, and their impact on target compounds such as alcohols, organic acids, and medium-chain fatty acids. Case studies illustrate how engineering approaches like bioreactor design, growth control, and product stabilization strategies can mitigate these challenges. The need for integrated solutions that combine improved feedstock utilization, process optimization, and carbon valorization pathways is emphasized to realize scalable, economically viable biomass biomanufacturing. The work highlights critical gaps and provides insight into future directions for maximizing carbon retention and achieving sustainable bioproduction systems.