Ultrasound-assisted extraction in water of betalains from selected colored quinoa hulls with specific colors was optimized by response surface methodology using a Box-Benhken design and then the thermal stability of these betalains was evaluated. Betacyanins from quinoa hulls were optimally extracted at amplitude = 70%, cycle = 0.6 and very short extraction time = 9.2 s, which produced 96.477 mg of betalains/100 g fresh weight of sample (FW). For quinoa hulls containing betaxanthins, an amplitude = 90%; cycle = 0.7 and extraction time = 40 s was required for the optimal extraction of pigments (201.01 mg of betalains/100 g FW). Total content of saponins between 0.69 and 1.14 mg/g FW, and 0.51 and 0.62 mg/g FW were found in the extract of betacyanins and betaxanthins, respectively. Conventional extraction of betalains from quinoa hulls required 30 min at room temperature to reach similar yields. The thermal stability kinetic parameters at 90 °C (first-rate rate constant, k = 0.068 min−1 and half-time, t1/2 = 10.2 min) for betacyanins extracted from quinoa hulls were comparable to those measured for beetroot betalains whereas betaxanthin extracted from quinoa hulls was more thermostable with a k = 0.019 min−1 and t1/2 = 37 min. Quinoa hulls are a good source of betalains and the presence of saponins in the extracts could help produce a unique bifunctional ingredient for the food and/or pharmaceutical industries.