Anthocyanins are widely used in the food industry for their intense colours and health benefits, such as cardiovascular protection and neuroprotection. However, their instability challenges large-scale applications. Clitoria ternatea flowers contain intense blue polyacylated anthocyanins that attract scientific interest. This study investigated the effects of an optimised anthocyanin extract (CTE) from C. ternatea blue petals on behavioural and neurochemical changes induced in Drosophila melanogaster by the herbicide paraquat, simulating a Parkinson’s disease model. Extraction by maceration was optimised using a Box-Behnken design, keeping pH and solid-liquid ratio constant, while varying time, ethanol concentration, and temperature. Total anthocyanins were quantified by HPLC. Based on Response Surface Methodology, CTE was added to the diet of D. melanogaster (up to 3 days old) for 10 days across five groups: standard control diet (SCD) and SCD with 0.5, 1.5, 5, and 15 mg/mL of CTE to find the ideal concentration. Behavioural studies (negative geotaxis and open field) and survival analyses identified 15 mg/mL as the optimal concentration. Consequently, flies were tested again with 15 mg/mL CTE for 10 days, introducing paraquat on the third day. Groups included: SCD control, SCD + CTE, SCD + paraquat, and SCD + paraquat + CTE. Results showed that 15 mg/mL CTE reduced fly mortality over treatment days and decreased climbing time compared to paraquat-exposed groups. No significant differences were observed in open field crossings. This study clarifies the impact of CTE on fly survival and locomotor behaviour.