TECHNOLOGY FOCUS - ORGANIC CHEMISTRY - Preferred Components: The biomass conversion system further comprises: a biomass feed mechanism operatively coupled to the hydrothermal digestion unit that allows a cellulosic biomass to be continuously or semi-continuously added to the hydrothermal digestion unit without the hydrothermal digestion unit being depressurized; a phase separation mechanism in fluid communication with the outlet of the second catalytic reduction reactor unit; a phase separation mechanism in fluid communication with an outlet of the first catalytic reduction reactor unit; and a flow control mechanism associated with each fluid circulation loop that allows a recycle ratio in each fluid circulation loop to be altered. The first catalyst comprises: a poison-tolerant catalyst, and is regenerable when poisoned with nitrogen compound impurities and/or sulfur compound impurities; or a sulfided catalyst. The second catalyst is not a poison-tolerant catalyst. In the biomass conversion system: the first catalytic reduction reactor unit comprises a fixed bed catalytic reactor; the first fluid circulation loop lacks a purification mechanism operable for removing nitrogen compound impurities and/or sulfur compound impurities; and the first fluid circulation loop is configured to establish countercurrent flow in the hydrothermal digestion unit. Preferred Method: In the method: heating the cellulosic biomass in the hydrothermal digestion unit takes place at a pressure of at least 30 bar, and in the presence of an organic solvent; the liquor phase is recirculated to the hydrothermal digestion unit so that countercurrent flow is established in the hydrothermal digestion unit; at least 60%, preferably at least 90% of the cellulosic biomass, on a dry basis, is digested to produce hydrolysate; providing a cellulosic biomass in the hydrothermal digestion unit comprises continuously or semi-continuously adding a cellulosic biomass to the hydrothermal digestion unit without the hydrothermal digestion unit being depressurized; after the cellulosic biomass is added to the hydrothermal digestion unit, the pressure in the hydrothermal digestion unit is at least 30 bar; and the liquor phase enters the first catalytic reduction reactor unit at a temperature of 120-190 degrees C and exits the first catalytic reduction reactor unit at 260-275 degrees C. The method further comprises: converting the first reaction product into a biofuel; monitoring the temperature of the liquor phase in the first fluid circulation loop; performing a phase separation of the first reaction product to form an aqueous phase and an organic phase; recirculating the aqueous phase to the hydrothermal digestion unit; transferring at least a portion of the first reaction product to the second fluid circulation loop; forming a second reaction product in the second catalytic reduction reactor unit; recirculating at least a portion of the second reaction product to the first fluid circulation loop at a second flow rate; converting the second reaction product into a biofuel; performing a phase separation of the second reaction product to form an aqueous phase and an organic phase; and recirculating at least a portion of the organic phase to the first fluid circulation loop. In the method, the first flow rate is so that the liquor phase: spends less than or equal to 3 hours in the hydrothermal digestion unit before being transferred to the first catalytic reduction reactor unit; and is recirculated in the first fluid circulation loop at a recycle ratio of at least 2, preferably 4-10. The second flow rate is so that: the second reaction product is recirculated to the first fluid circulation loop at a recycle ratio of at least 0.1, preferably 0.1-0.5; and a sufficient quantity of the second reaction product is recirculated to the first fluid circulation loop to inhibit lignins from precipitating, where the second reaction product comprises a higher percentage of organic compounds than it does water.