: It was postulated that a phytobiotic preparation containing cinnamon oil and citric acid added to drinking water for chickens in a suitable amount and for a suitable time would beneficially modify the microbiota composition and morphology of the small intestine, thereby improving immunity and growth performance without inducing metabolic disorders. The aim of the study was to establish the dosage and time of administration of such a phytobiotic that would have the most beneficial effect on the intestinal histology and microbiota, production results, and immune and metabolic status of broiler chickens. The experiment was carried out on 980 one-day-old male chickens until the age of 42 days. The chickens were assigned to seven experimental groups of 140 birds each (seven replications of 20 individuals each). The control group (G-C) did not receive the phytobiotic. Groups CT-0.05, CT-0.1, and CT-0.25 received the phytobiotic in their drinking water in the amount of 0.05, 0.1, and 0.2 mL/L, respectively, at days 1–42 of life (continuous application, CT). The birds in groups PT-0.05, PT-0.5, and PT-0.25 received the phytobiotic in the same amounts, but only at days 1–7, 15–21, and 29–35 of life (periodic application, PT). Selected antioxidant and biochemical parameters were determined in the blood of the chickens, as well as parameters of immune status and redox status. The morphology of the intestinal epithelium, composition of the microbiome, and production parameters of chickens receiving the phytobiotic in their drinking water were determined as well. The addition of a phytobiotic containing cinnamon oil and citric acid to the drinking water of broiler chickens at a suitable dosage and for a suitable time can beneficially modify the microbiome composition and morphometry of the small intestine (total number of fungi p < 0.001, total number of aerobic bacteria p < 0.001; and total number of coliform bacteria p < 0.001 was decreased) improving the immunity and growth performance of the chickens (there occurred a villi lengthening p = 0.002 and crypts deepening p = 0.003). Among the three tested dosages (0.05, 0.1, and 0.25 mL/L of water) of the preparation containing cinnamon oil, the dosage of 0.25 mL/L of water administered for 42 days proved to be most beneficial. Chickens receiving the phytobiotic in the amount of 0.25 mL/L had better growth performance, which was linked to the beneficial effect of the preparation on the microbiome of the small intestine, metabolism (the HDL level p = 0.017 was increased; and a decreased level of total cholesterol (TC) p = 0.018 and nonesterified fatty acids (NEFA) p = 0.007, LDL p = 0.041, as well as triacylglycerols (TAG) p = 0.014), and immune (the level of lysozyme p = 0.041 was increased, as well as the percentage of phagocytic cells p = 0.034, phagocytosis index p = 0.038, and Ig-A level p = 0.031) and antioxidant system (the level of LOOH p < 0.001, MDA p = 0.002, and the activity of Catalase (CAT) p < 0.001 were decreased, but the level of ferric reducing ability of plasma (FRAP) p = 0.029, glutathione p = 0.045 and vitamin C p = 0.021 were increased).