Intermediates produced following deconstruction of biomass include bio-oils, gaseous mixtures such as synthetic gas (syngas), sugars, and other chemical building blocks. These intermediates are upgraded using various techniques to produce a finished product. These finished products could be fuels or bioproducts, or they could be stabilized intermediates suitable for finishing in a petroleum refinery or chemical manufacturing plant. 

Actual upgrading and separation processes will vary greatly according to the identity of the intermediate streams. Streams with tight chemical distributions may require less complex processes than streams involving more varied compounds. Chemical rearrangement into the final fuel blendstock or product can involve biological or chemical processing. 

Microorganisms can ferment intermediates into fuel blendstocks and chemicals, while catalysts can be used to process other intermediate streams, such as bio-oil and syngas. Intermediate processing minimizes the effect of reactive compounds to improve storage and handling properties.