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The assessment of protein quality using an <i>in vitro</i> methodology may be a suitable replacement for <i>in vivo</i> models to generate digestibility in pulses and cereals. In this study, two varieties of soy, wheat and oat flour, that remained untreated or cooked, were investigated using a rat bioassay. Sprague Dawley rats (n=130, ~70g) were randomized to one of twelve diets corresponding to either variety of Etna/Amadeus soy (ES/AS), Carberry/Snowbird wheat (CW/SW), Turcotte/Navaro oat (TO/NO) flour, as well being untreated or cooked, with casein as a control. Protein quality <i>in vivo</i> was assessed using the protein efficiency ratio (PER), true protein digestibility (TPD) and protein digestibility corrected amino acid score (PDCAAS). A pH drop method was used to calculate <i>in vitro</i> protein digestibility (IVPD) and <i>in vitro</i> protein digestibility corrected amino acid score (IVPDCAAS). The PER of cooked ES (2.12), AS (2.06), CW (1.11) and SW (1.22) increased over their untreated equivalent, whereas the PER of untreated TO (2.03) and NO (2.23) increased over their cooked equivalent. The PDCAAS of AS was lower (56.9) than ES (75.0), due to a greater methionine and cysteine content (17.5, 21.9 mg/g protein; respectively) in the ES. Overall, ES, CW, SW, TO and NO had increased PDCAAS values when cooked over untreated. Analysis of correlation revealed an association between TPD and IVPD (R2= 0.7013 p<0.0001), while a significant correlation was found between PDCAAS and IVPDCAAS (R2=0.9697 p<0.0001). The strong correlation between <i>in vivo</i> and <i>in vitro</i> methodology suggests that it may be a sensitive, inexpensive and ethical replacement method for animal bioassays in evaluating protein quality.