Vegetarian diets provide an abundance of nutrients when carefully planned. However, vegetarian diets may have lower protein quality compared to omnivorous diets, a reflection of less favorable amino acid profiles and bioavailability. Hence, the current recommended dietary allowance for protein may not be adequate for some vegetarian populations. The purpose of this study was to determine dietary protein quality using the DIAAS (Digestible Indispensable Amino Acid Score) method in vegetarian and omnivore endurance athletes. DIAAS scores reflect the true ileal digestibility of the indispensable amino acids that are present in food items, and these scores can be used to compute the available protein in diet plans. Thirty-eight omnivores and 22 vegetarians submitted seven-day food records that were analyzed for nutrient content, and DIAAS scores were computed by diet group. Average available protein (g) was compared along with participants’ lean body mass and strength (quantified using the peak torque of leg extension). DIAAS scores and available protein were higher for omnivorous versus vegetarian athletes (+11% and +43%, respectively, p < 0.05). Omnivorous participants had significantly higher lean body mass than vegetarian participants (+14%), and significant correlations existed between available protein and strength (r = 0.314) and available protein and lean body mass (r = 0.541). Based upon available protein, as determined through the DIAAS, vegetarian athletes in this study would need to consume, on average, an additional 10 g protein daily to reach the recommended intake for protein (1.2 g/kg/d). An additional 22 g protein daily would be needed to achieve an intake of 1.4 g/kg/d, the upper end of the recommended intake range.