The life cycle of Plasmodium has three phases: the asexual pre-erythrocytic and erythrocytic stages in humans, and the sexual stage in mosquitoes. Although the stages within the human host are well documented, the early bottleneck ookinete stage, occurring within the first 24 hours after the parasite enters the mosquito, remains less understood. Upon taking in blood meal from a parasite-infected host, male and female gametes merge to create a zygote, which eventually develops into a motile and invasive ookinete that penetrates the peritrophic matrix and midgut, while also evading the mosquito's immune responses. The advancement of the parasite aligns with the digestion of the mosquito's blood meal, essential for egg development, facilitated by enzymes. This study investigates the role of carboxypeptidase B (CPB) and peritrophin 48 (Per48) during Plasmodium transmission in Anopheles stephensi, and explores their potential molecular interactions. To evaluate mRNA and miRNA expression profiles in the mosquito midgut tissues, high-throughput sequencing was employed under four experimental conditions: infected (IBF) and uninfected (BF) samples at 18 and 24 h post blood feeding. mRNA analysis revealed significant changes in gene expression, with 1,366 upregulated and 800 downregulated genes at 18 h post-infection, which shifted to 1,780 upregulated and 204 downregulated genes at 24 h. Within this expression profile, both Per48 and CPB were downregulated in infected samples at 18 h, which was confirmed by qRT-PCR analysis. Additionally, miRNA sequencing identified 22 known miRNAs and 12 novel miRNAs, with a rise in the expression of ast-miR-2944 and ast-miR-29a. In silico analysis of miRNA-mRNA interactions suggested that the increased miRNA expression could lead to the downregulation of CPB and Per48. Further, molecular docking showed high binding affinity between Per48 and CPB. This study establishes that Per48 and CPB, in a coordinated manner, influence both digestion and parasite transmission during the early infection phase, offering new insights into vector--parasite interactions and potential targets aimed at blocking transmission.