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Cooking time is a crucial determinant of culinary quality of cassava roots and incorporating it into the early stages of breeding selection is vital for breeders. This study aimed to assess the potential of near-infrared spectroscopy (NIRS) in classifying cassava genotypes based on their cooking times. Five cooking times (15, 20, 25, 30, and 40 minutes) were assessed and 888 genotypes evaluated over three crop seasons (2019/2020, 2020/2021, and 2021/2022). Fifteen roots from five plants per plot, featuring diameters ranging from 4 to 7 cm, were randomly chosen for cooking analysis and spectral data collection. Two root samples (15 slices each) per genotype were collected, with the first set aside for spectral data collection, processed, and placed in two petri dishes, while the second set was utilized for cooking assessment. Cooking data were classified into binary and multiclass variables (CT4C and CT6C). Two NIRs devices, the portable QualitySpec® Trek (QST) and the benchtop NIRFlex N-500 were used to collect spectral data. Classification of genotypes was carried out using the K-nearest neighbor algorithm (KNN) and partial least squares (PLS) models. The spectral data were split into a training set (80%) and an external validation set (20%). For binary variables, the classification accuracy for cassava cooking time was notably high ( R C a l 2 ranging from 0.72 to 0.99). Regarding multiclass variables, accuracy remained consistent across classes, models, and NIR instruments (~0.63). However, the KNN model demonstrated slightly superior accuracy in classifying all cooking time classes, except for the CT4C variable (QST) in the NoCook and 25 min classes. Despite the increased complexity associated with binary classification, it remained more efficient, offering higher classification accuracy for samples and facilitating the selection of the most relevant time or variables, such as cooking time ≤ 30 minutes. The accuracy of the optimal scenario for classifying samples with a cooking time of 30 minutes reached R C a l 2   = 0.86 and R V a l 2 = 0.84, with a Kappa value of 0.53. Overall, the models exhibited a robust fit for all cooking times, showcasing the significant potential of NIRs as a high-throughput phenotyping tool for classifying cassava genotypes based on cooking time., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Bandeira e Sousa, Morales, Mbanjo, Egesi and Oliveira.)