Aqueous phase (AP) is frequently observed in bio-oil from biomass thermochemical conversion or as an upgrading coproduct. However, AP contains high organic content that can be toxic and that must be reduced or removed to be then treated in existing wastewater plants. A promising method to upgrade these APs is the catalytic wet peroxide oxidation (CWPO) that was applied here on APs of both hydrothermal liquefaction and pyrolysis bio-oils from softwood and hardwood. Efficiency of the CWPO was assessed by investigating the molecular composition of raw and treated APs by ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with electrospray ionization (ESI) in negative- and positive-ion modes. Combination of FT-ICR MS and multivariate statistical analyses evidenced efficiency of the process with new compounds resulting from the oxidative depolymerization, characterized by lower unsaturation degree and molecular weight, and higher oxygen atom count. Refractory compounds were also observed, which are notably characterized by high unsaturation degrees. Interestingly, both detection modes were shown to be complementary for the understanding of the CWPO process. ESI (-) allowed to assess the completion of the oxidation process in detecting carboxylic acid conversion products and to specifically evidence refractory products. ESI (+) was informative on the CWPO process, especially on the conversion of the basic compounds, with the decrease of the detected species. Eventually, softwood AP was shown to be more reluctant to CWPO than the hardwood one.