The objective of this study was to evaluate the physicochemical, textural, sensory and microbiological stability of cupcakes during storage after the addition of different proportions of quinoa protein isolate modified by heat denaturation (QPI-HD) and freezing-lyophilization (QPI-FL). The cupcakes containing modified quinoa protein exhibited greater firmness and water activity than the control cupcake. The texture profile analysis (TPA) revealed that the cupcakes with modified quinoa protein were statistically different from those with unmodified protein isolate and the control cupcake. Moreover, cupcakes with quinoa protein modified by either heat or freezing had greater acceptance and preference on the part of consumers. In addition to this, these cupcakes showed lesser growth of molds after 10 days of storage; this indicated that the abovementioned additive could extend the shelf life of cupcakes. These results showed that the addition of modified quinoa protein led to cupcakes with better sensory and textural properties and greater stability during storage.