Fortification of food with iron is considered to be an effective approach to counter the global health problem caused by iron deficiency. However, reactivity of iron with the catechol moiety of food phenolics leads to discolouration and impairs bioavailability. In this study, we investigated the interplay between intrinsic and extrinsic factors on food discolouration caused by iron-catechol complexation. To this end, a three-level fractional factorial design was implemented. Absorbance spectra were analysed using statistical methods, including PCA, HCA, and ANOVA. Furthermore, a direct link between absorbance spectra and stoichiometry of the iron-catechol complexes was confirmed by ESI-Q-TOF-MS. All statistical methods confirm that the main effects affecting discolouration were type of iron salt, pH, and temperature. Additionally, several two-way interactions, such as type of iron salt × pH, pH × temperature, and type of iron salt × concentration significantly affected iron-catechol complexation. Our findings provide insight into iron-phenolic complexation-mediated discolouration, and facilitate the design of iron-fortified foods.