Biomass-based products (bioproducts) have been introduced as a means to address food-energy-water nexus challenges. However, the existing approaches have not been integrated to convert biomass into market-competitive bioproducts (e.g., biochar and bio-oil). Pretreatment and conversion processes represent the most substantial portion of the total bioproduct cost. This study proposes a portable conversion process for high-quality biochar and bio-oil production, using mixed reactors and advanced cyber-physical infrastructures to promote cross-cutting technological and commercialization opportunities. The proposed portable process converts biomass to bioproducts near the collection sites, which can address collection, staging, and logistics challenges. The fundamental novelty of this study lies in utilizing cyber-physical technologies for advancing pre-/post-conversion processes and crossing the boundaries to meet the market needs. A case study for biochar production from various biomass feedstocks is used to demonstrate and verify the application of the conversion process and the cyber-based advances. The results indicate that the integrated cyber-physical conversion pathway can increase process yield and quality. It is also found that biomass properties and conversion process configurations play a crucial role in determining the process yield and biochar quality in terms of the physical-chemical structure.