Two genotypes of pigmented maize (black (BM) and red (RM)) were used as flour ingredients in several formulations of the traditional baked maize dish "proja". This study investigated the stability of phytochemical compounds and antioxidant activity in proja as affected by baking and different acidity degrees of dough formulations. Compared to RM proja, all BM proja formulations were significantly higher in antioxidant compounds and exhibited the highest inhibitory activity (73-85%) against DPPH. There was a strong significant correlation between DPPH inhibition and total phenolics (r2 = 0.95), flavonoids (r2 = 0.96), and anthocyanins (r2 = 0.97) in baked proja. After baking, 67-85% of total phenolics were retained. The fate of flavonoids and anthocyanins after baking was variable: from 70% degradation to liberation. Dough acidity significantly and positively affected the content of phenolics, flavonoids, and anthocyanins in BM proja (r2 = 0.70, 0.82, and 0.47, respectively). Baking increased antioxidant activity against DPPH, •OH, and O2•- radicals in proja, except for ≈10% decline of DPPH inhibition in BM proja. In RM proja, retention of inhibitory capacity against O2•- was highly correlated to flavonoid retention (r2 = 0.71). Using pigmented maize flour in proja baking resulted in proja with appreciable content of total phenolics, flavonoids, anthocyanins, and high antioxidant activity, confirming the significant improvement of the nutrient profile of this traditional food.