Rapid single kernel analysis could enable physical sorting to remove mycotoxins from bulk grains. The purpose of this study was to use visual characteristics previously associated with aflatoxin and fumonisin contamination of maize kernels to calibrate a multi-spectral sorter and then sort mycotoxin contaminated lots. A total of 76 corn samples were collected from poultry farmers in the Dorma-Ahenkro area, Ghana. Paired 400-g subsamples were used for bulk analysis and single kernel sorting. Individual kernels were selected from contaminated samples by 2 levels of stratification: visible high-risk kernels (n = 1000) and visible low risk kernels (n = 1000). High-risk kernels had one or more of 3 features: fluorescence under UV (366 nm) light, mold, or brokenness. Kernels were used to calibrate a multi-spectral sorter (individual wavelengths from 470 to 1070 nm) to remove high-risk kernels. Then, kernel samples were sorted and the reject and accept streams individually ground and tested for aflatoxin and fumonisin contamination using ELISA. Bulk sample levels ranged between 0.78 and 67 ppb aflatoxin and <2.5 × 10−3 – 5.7 ppm fumonisin. Classification algorithms to reject visible high-risk spectra were 63% sensitive and 90% specific. After sorting, samples showed a significant aflatoxin reduction (p < 0.001, 73/76 samples reduced, mean reduction 31 ppb, range −9.7 – 67 ppb); all samples showed a significant fumonisin reduction (p < 0.001, mean reduction 1.9 ppm, range 9.3 × 10−2 – 6.1 ppm). From the accepted stream, 61/76 samples tested <15 ppb aflatoxin, significantly more than the 40/76 prior to sorting (p < 0.001); all accepted samples tested <2 ppm fumonisin concentration compared to only 2/76 prior to sorting. From sorting, average mass rejected was 12% (range 1.2%–36%), and that rejected mass contained an average of 46% of the total aflatoxin (range 4.3%–97%) and 88% of the total fumonisin (range 10%–84%). Visual characteristics associated with mycotoxin contamination can inform classification models which can enable sorting contaminated maize to reduce aflatoxin and fumonisin contamination.