The objective was to evaluate the effect of near infrared spectroscopy instrumentation with NIRS FOSS and Perten on predictions of crude protein (CP) and in vitro dry matter digestibility (IVDDM) and in vitro organic matter digestibility (IVDOM) of cottonseed. The models for the CP parameter obtained better results in the NIR Perten and FOSS instruments than the models for IVDDM and IVDOM of cottonseed. In addition, the model with the best performance observed for CP was attributed to NIR Perten, considering its best RPD index.