Physical methods for mechanically in-shell Brazil nut sorting by color, size, density and inner deterioration were developed to assess nut quality and reduce aflatoxin contamination. Nuts were able to be sorted by color utilizing the standard shell chromaticity components L*, a* and b* at ranges of 31.51 to 48.64, 4.09 to 10.07 and 11.90 to 22.95, respectively. It produced a homogeneous color batch and segregated the off-standard ones (darkest, lightest and stained). By size sorting utilizing three oval sectioned trays with the following dimensions 40x25, 35x23 and 20x19.5 mm [length x width] and vibration, nuts were sorted into three sizes Groups: I, II and III for large, medium and small, respectively. Through density sorting the light nuts (shell/nut <1.5) which have inner mass reduction by fungi growth and/or dehydration, were separated with two compressed air streams from the healthy ones. Utilizing near infrared (NIR) spectrophotometry, the nuts inner deterioration was detected, with no need of de-shelling them at the wavelength range of 2200 to 2500 nm. Any nut measurement detected, lower or higher than those sorting settings, was considered off-standard and rejected. Pools of the final standard and off-standard nuts were analyzed for aflatoxins by LC-MS/MS. No toxin was detected in the final standard batch up to the method LOQ (0.08, 0.09, 0.10 and 0.12 μg/kg for AFB 1 ,AFB 2 , AFG 1 , AFG 2 , respectively). On the other hand, the off-standard rejected batch had 16.4 μg/kg of AFB 1 . These methods are important tools for building an in-shell Brazil nut sorting machine to assess nut quality and reduce aflatoxin contamination.