The development of efficient processes for the upgrading of low value bio-derived liquid intermediates to high added value products in biorefineries is critical for the establishment of a robust and competitive bio-based economy. We show in this paper that low quality surrogate heavy naphtha, representative of biofuels from thermochemical biomass conversion processes, can be efficiently converted to high quality fuel and chemicals (olefins) via hydroisomerization and catalytic cracking, respectively. Hydroisomerization over a low loading 0.1 wt% Pt/ZSM-5 catalyst leads to the conversion of normal paraffins to C5-C8 isoparaffins with limited cracking, and produces a fuel with higher octane and lower cetane number, suitable for use in future powertrains such as HCCI engines. Catalytic cracking of the naphtha on a commercial ZSM-5 based FCC catalyst results in the production of a significant amount of olefins at 600 degrees C, primarily propylene followed by ethylene, n-butene, pentene and i-butene. Both processes are validated on pilot scale. Some differences observed between bench and pilot scale results are due to scalability phenomena and different reaction conditions. Still, excellent agreement with regards to the composition of the products at similar conversion level exists, demonstrating the scalability and applicability of these upgrading processes in thermochemical biorefineries.