This work aimed to investigate the bio-distribution and the persistence of fipronil and its primary metabolite fipronil sulfone after oral and dermal administration by simulating natural farming conditions. Fipronil and fipronil sulfone detection and quantification were performed in different poultry matrices using an LC-MS/MS method coupled with modified QuEChERS extraction. After oral administration, fipronil was detected in feathers at each sampling time, in eggs for 28 days, and in the internal organs at the end of the experiment. After dermal administration, high levels of fipronil were detected in feathers, accounting for 195.85 ± 8.54 mg/kg, which were reduced by a third after 60 days. No traces of fipronil were detected in the eggs or internal organs. In addition, fipronil sulfone showed remarkable residues in all samples in trial 2. The data obtained confirmed that inappropriate use of unauthorized pesticides can lead to severe contamination of entire poultry farms. The contemporary presence of fipronil sulfone in feathers and eggs associated with the lack of fipronil in eggs suggests recent dermal contamination or past oral contamination. Moreover, simultaneous analysis of hens’ feathers and eggs could represent a new method to improve large-scale monitoring programs and animal welfare, limiting their slaughter.