The Fenton reaction is an effective advanced oxidation process occurring in nature and applied in engineering processes toward the degradation of harmful substances, including contaminants of emerging concern. The traditional Fenton application can be remarkably improved by using iron complexes with organic ligands, which allow for the degradation of contaminants at near-neutral pH and for the reduction of sludge production. This work discusses the mechanisms involved both in the classic Fenton process and in the presence of ligands that coordinate iron. Cyclohexane was selected as mechanistic probe, by following the formation of the relevant products, namely, cyclohexanol (A) and cyclohexanone (K). As expected, the classic Fenton process was associated with an A/K ratio of approximately 1, evidence of a dominant free radical behavior. Significantly, the presence of widely common natural and synthetic carboxyl ligands selectively produced mostly the alcoholic species in the first oxidation step. A ferryl-based mechanism was thus preferred when iron complexes were formed. Common iron ligands are here proven to direct the reaction pathway towards a selective metal-based catalysis. Such a system may be more easily engineered than a free radical-based one to safely remove hazardous contaminants from water and minimize the production of harmful intermediates.