The growing demand for functional foods and the need to reduce agri-food waste have encouraged the use of natural ingredients derived from agro-industrial by-products, promoting the circular economy and the development of foods with enhanced nutritional and technological properties. This study aimed to evaluate the effect of incorporating beetroot stem flour (BSF) at concentrations of 1% (R1%) and 3% (R3%), compared with a control sample (CNT) without BSF, on pH, color parameters, and antioxidant activity (DPPH) of fresh gluten-free pasta. The results showed that BSF incorporation did not significantly affect pH, with values of 6.48 ± 0.08 for CNT, 6.38 ± 0.04 for R1%, and 6.31 ± 0.06 for R3%, although a slight decrease was observed as the BSF concentration increased. Lightness (L*) decreased from 75.26 ± 0.17 in CNT to 42.87 ± 1.30 in R1% and 37.00 ± 1.24 in R3%, indicating progressive darkening. This was accompanied by an increase in the a* parameter, from −1.17 ± 0.48 in CNT to 29.25 ± 0.73 in R1% and 34.66 ± 0.39 in R3%, reflecting a greater intensity of red hues associated with the betalains naturally present in BSF. Likewise, the b* parameter decreased from 9.68 ± 0.55 in CNT to 1.43 ± 0.54 in R1% and 2.39 ± 0.06 in R3%, indicating a reduction in yellow tones and a shift toward red and purple coloration. The DPPH, values increased from 0.739 mmol/100 g in CNT to 1.37 mmol/100 g in R1% and 2.21 mmol/100 g in R3%. Both R1% and R3% exhibited greater free radical scavenging capacity than the control, confirming the contribution of betalains to the antioxidant potential of the pasta. In conclusion, beetroot stem flour improves the functional properties and color of fresh gluten-free pasta by enhancing its antioxidant activity and imparting a natural red coloration, highlighting its potential as an alternative to synthetic colorants. Furthermore, its use contributes to the valorization of agro-industrial by-products and supports the circular economy through the development of sustainable functional foods.