Whole wheat pasta is rich in fiber and antioxidants, but presents dark color and altered cooking characteristics. This study aimed to evaluate the effects of yellow (YNC) and pink (PNC) natural concentrates in fresh whole wheat pasta, on its fiber content, and technological, and antioxidant properties. Control pasta (CP) was prepared (70:30 w:w whole grain wheat (WGF): refined wheat flour (RWF)). YNC and PNC were applied (1 to 2 g/100 g) in pastas containing 60 to 70 g/100 g of WGF, following a 22 experimental design, with three central points. YNC and PNC modified whole wheat pastas color, without altering their technological characteristics. Yellow pasta (YP1, 60:40 WGF:RWF w:w, 1 g YNC/100 g) and pink pasta (PP9, 70:30 WGF:RWF w:w, 1 g PNC/100 g) presented similar texture, weight gain and cooking loss to CP, and they were selected for antioxidants analysis. The three pastas had high fiber content (above 6 g/100 g), and PNC caused a significant increase in total phenolics content in raw and cooked whole wheat pasta. The natural-colored concentrates are an alternative for modifying the color of whole wheat pasta while adding functional value to it.