We demonstrate that removal of oxygen and metals from crude algae oils produced by hydrothermal treatment processes is possible by thermal means alone and without the use of catalysts or hydrogen. Thermal treatment can reduce the total amounts of acids in the crude algae oil and thus decrease the total acidity of the oil. Thermal treatment also reduces the boiling point range of crude algae oils, making them more volatile and less viscous, benefitting shipping and upgrading. Trace metals are significantly reduced as the thermal treatment temperature increases. The results obtained in this study are consistent with existing theories of the formation of petroleum crude oils and create a link between the upgrading of crude algae oils and the mechanisms involved in the formation of conventional fossil fuels. The results and possible pathways of the reaction mechanisms are presented.