A great diversity of fruits is used in the food industry to obtain different products such as juices, sauces and foods. However, the food industry produces high amounts of residues. Passion fruit and guava are worldwide known fruits and very used by the food industry and generate tons of seed as residue. This work aims to study the extraction of oils from passion fruit and guava juice industries residues, their characterization and potential application as raw materials to obtain biodiesel and bio-oil. The passion fruit and guava seed oils content were 25 and 9%, respectively. In both oils, polyunsaturated fatty acids are predominant. Biodiesel obtained by esterification/transesterification of both seed oils match most of the parameters specified for biodiesel in Brazil. Bio-oils obtained by thermal cracking of the seed oils were mainly composed by hydrocarbons similar to those observed in petroleum diesel.