The objective of the present work was to optimize the microencapsulation conditions of neem (Azadirachta indica A. Juss) leaf extracts for the biocontrol of Tenebrio molitor. The complex coacervation method was used for the encapsulation of the extracts. The independent factors considered were the pH (3, 6, and 9), pectin (4, 6, and 8% w/v), and whey protein isolate (WPI) (0.50, 0.75, and 1.00% w/v). The Taguchi L9 (33) orthogonal array was used as the experimental matrix. The response variable was the mortality of T. molitor after 48 h. The nine treatments were applied by immersion of the insects for 10 s. The statistical analysis revealed that the most influential factor on the microencapsulation was the pH (73% of influence), followed by the pectin and WPI (15% and 7% influence, respectively). The software predicted that the optimal microencapsulation conditions were pH 3, pectin 6% w/v, and WPI 1% w/v. The signal-to-noise (S/N) ratio was predicted as 21.57. The experimental validation of the optimal conditions allowed us to obtain an S/N ratio of 18.54, equivalent to a T. molitor mortality of 85 ± 10.49%. The microcapsules had a diameter ranging from 1–5 μm. The microencapsulation by complex coacervation of neem leaf extract is an alternative for the preservation of insecticidal compounds extracted from neem leaves.