Bark of acuri and endocarp of baru are residues generated during the processing of these fruits. One alternative to consider is the pyrolysis of these materials to generate bio-oils, opening the perspective for the production of environment-friendly, added value products. Samples of acuri and baru were subjected to laboratorial scale pyrolysis. At the optimized pyrolysis conditions, the bio-oils yields (m/m) were 30% for bark of acuri and 29% for endocarp of baru. Next, the obtained bio-oil was submitted to proximate analysis and GC×GC-TOF/MS (two-dimensional gas chromatography with time-of-flight mass spectrometric detection). The bio-oil generated from the bark of acuri proved to be of the highest complexity with 113 identified compounds, while the bio-oil generated from the endocarp of baru sample led to 71 identified compounds. A total of 29 compounds were confirmed using standards in the acuri bark bio-oil, while 23 compounds were confirmed for endocarp of baru bio-oil. There was a predominance of phenols and ketones for the bio-oil generated from acuri bark, and hydrocarbons and phenols for the bio-oil from baru endocarp.