Fortification of foods with phenolic compounds is becoming increasingly popular due to their beneficial physiological effects. The biological activities reported include antioxidant, anticancer, antidiabetic, anti-inflammatory, or neuroprotective effects. However, the analysis of polyphenols in functional food matrices is a difficult task because of the complexity of the matrix. The main challenge is that polyphenols can interact with other food components, such as carbohydrates, proteins, or lipids. The chemical reactions that occur during the baking technologies in the bakery and biscuit industry may also affect the results of measurements. The analysis of polyphenols found in fortified foods can be done by several techniques, such as liquid chromatography (HPLC and UPLC), gas chromatography (GC), or spectrophotometry (TPC, DPPH, FRAP assay etc.). This paper aims to review the available information on analytical methods to fortified foodstuffs while as presenting the advantages and limitations of each technique.