Background: Phytogenic compounds are one of many alternatives to current industry feed ingredients for the poultry industry. However, despite increased reports on the activity of phytogenic compounds against disease in poultry, there is a lack of data regarding safety and residual toxicity. This two-part study investigated the general health of broiler chickens fed Berberine, Ursolic Acid, Piceid, Honokiol and Baicalin in-feed at three different levels, and assessed the poultry tissue residue of Berberine in breast muscle, upper and lower thigh, and liver through LC/MS-MS. Methods and Findings: Phase 1 trial results demonstrated that all birds appeared normal, with all gastrointestinal histologic lesions and liver histologic lesions identified within normal limits for broiler chickens in a production environment. Phase 2 trial showed that the lowest amount of Berberine, 0.03 g/kg in-feed, resulted in tissue residues below the lower limit of detection (<2 ng/g), and the highest amount of Berberine, 0.3 g/kg in-feed, yielded detectable values, although the significance of these results is still not clear. Conclusions: In conclusion, the present study suggests that the five tested phytogenic compounds are safe for use in starter, grower and finisher feeds for broiler chickens. Further exposure and risk assessment calculations regarding appropriate residue levels are necessary to evaluate the use of Berberine as a feed ingredient for poultry.