Due to increasing concerns about the contamination of animal food products with antibiotic-resistant bacteria and their byproducts, phytogenic feed additives in animal diets have been explored as antibiotic alternatives. In this study, we investigated the effect of ginger root extract (GRE), green tea extract (GTEC caffeinated and GTED decaffeinated), and onion peel combined (OPEC) on the activity of C. perfringens toxin genes and Eimeria tenella sporozoites. To this end, two Clostridium perfringens strains, CP19 and CP240 (Rollins Diagnostic Lab, Raleigh, NC, USA), were cultured (three replicates per treatment) as follows: without additives (Control), with Bacitracin Methylene Disalicylate (BMD), with GRE, with GTEC, with GTED, and, finally, with OPEC for 0, 2, 4, 6, 8, and 24 h. RNA was extracted to determine the expression of tpeL, alpha toxin (α-toxin), and NetB and we measured the protein concentration of NetB-positive C. perfringens toxin. Also, we evaluated the cytotoxic effect of green tea and ginger extracts on E. tenella sporozoites. Results show that phytogenic extracts, GRE, GTEC, and GTED, significantly reduced (p < 0.05) the level of expression of α-toxin gene compared to control; however, BMD treatment showed much less effect. Furthermore, NetB and tpeL encoding gene expression was significantly (p < 0.05) reduced by GRE and GTED, as well as BMD treatment, compared to the control. In contrast, GTEC treatment did not change the expression levels of these genes and was similar to control. With the CP240 strain, all the selected phytogenic extracts significantly reduced (p < 0.05) the expression of selected genes, except for OPEC, which was similar to control. GRE, GTEC, and GTED all reduced the viability of concentration of E. tenella sporozoites. Overall, our data show that these selected phytogenic extracts reduced the level of expression of toxin encoding genes associated with necrotic enteritis and decreased the viability of sporozoites which cause coccidiosis in broiler chicken.