A system and process are described for clean separation of biocrudes and water by-products from hydrothermal liquefaction (HTL) product mixtures of organic and biomass-containing feedstocks at elevated temperatures and pressures. Inorganic compound solids are removed prior to separation of biocrude and water by-product fractions to minimize formation of emulsions that impede separation. Separation may be performed at higher temperatures that reduce heat loss and need to cool product mixtures to ambient. The present invention thus achieves separation efficiencies not achieved in conventional HTL processing.