The pecan (Carya illinoinensis) tree has adapted to the South of Brazil and has been consolidating like an important crop, generating income and diversification in the rural properties. However, the harvest is seasonal and concentrated in April and May, needing to storage the major part of the production. Studies on nut storage, specifically in controlled atmosphere (CA), are still incipient. Thus, in this study was evaluated the storage of nuts in shell (Barton cultivar) at different concentrations of O2 (1, 3 and 20%-Atmospheric air-AA) and temperature (1.5, 10 and 20 °C). On initial and after 6 months of storage were analyzed oxidation markers (OM) (peroxidation index-PI and acidity index-AI) and changes in volatile compounds (CVs) by gas chromatography coupled to mass spectrometry. The oxidative process was most accelerated at the highest temperature (20 °C). Thus, AA-1.5 °C treatment presented the better result of OM, with AI of 0.34 meq (oleic acid) and IP of 1.73 meqO2/kg in relation to the initial time. On the other hand, AA-20 °C treatment changed the parameters to AI 0.90 meq and IP 1.85 meqO2/kg. Other treatments when in the lower temperatures, did not present significant difference (p>0.05) among themselves for OM. Concerning CVs, all treatments submitted to 20 °C also showed an increase in the chemical classes of the acids (C2 to C9), alcohols (C2 to C9, phenylethylic and benzylic), aldehydes (C6 to C9) and furans (only in AR-20 °C), coming mainly from lipid oxidation, but some from aminoacids and carbohydrates degradation. The significant increase of hexanal, octanal, hexanoic acid and nonanoic acid may contribute with rancid sensory notes, implying negatively to sensory quality. Finally, low temperature storage showed better results in relation to deterioration indicators, showing that at 20 °C of temperature there is need to preserve nuts at lower oxygen concentrations.