Pigmented rice bran is under-researched for human nutrition. This study investigated milling and cooking effects on the physicochemical and nutritional quality of pigmented and non-pigmented rice. Raw rice properties, cooking behavior and nutritional in-vitro quality were evaluated. Samples were cooked following a “risotto” preparation method. Bran removal by milling reduced kernel dimension (15%) and hardness (8%). Pigmented rice had higher total phenolic content (TPC; >41%) and higher antioxidant activity (AOA; >24%) than Carnaroli but milling significantly (p ≤ 0.05) reduced them. The bran was fractionated and (re)added during rice cooking as a new strategy to preserve nutritional compounds at their best. Compared with brown rice, milled samples exhibited greater geometric expansion and shorter cooking times (>47%), confirming that removal of the outer layer facilitated water penetration. Cooking affected the TPC differently depending on the rice variety (e.g., -15.5% for Violet and +7.8% for Orange brown samples). The incorporation of rice bran during cooking improved the “risotto” color and its nutritional value (TPC > 53% and AOA > 60%). Results evidenced the impact of different processing methods on rice quality, suggesting the potential use of rice co-product (i.e., bran) as new ingredient for healthier and more sustainable foods.