The influence of a commercial production process for dehydrated potato flakes on the content of free phenolic compounds, total phenolics, and glycoalkaloids in potatoes during the subsequent processing steps was determined. Processing byproducts, such as potato peel (steam peeling), mashed potato residues, and side streams (blanching and cooking waters), have also been investigated. A high-performance liquid chromatography (HPLC) method was developed to separate and quantify caffeic acid, gallic acid, ferulic acid, p-coumaric acid, p-hydoxybenzoic acid, protocatechuic acid, vanillic acid, catechin, and three isomers of caffeoylquinic acid: chlorogenic, neochlorogenic and cryptochlorogenic acid. Determination of the glycoalkaloids alpha-solanine and alpha-chaconine was performed by using a high-performance thin-layer chromatography (HPTLC) method. The deliverables reveal that processing potatoes to potato flakes remarkably diminishes the content of the analyzed compounds, mainly due to peeling and leaching. The influence of thermal exposure is less significant. About 43% of the initial phenolic acids and 10% of the glycoalkaloids remain after processing. The results of the total phenolic content assay by Folin-Ciocalteu reagent are proportional to the content of phenolic compounds determined by HPLC. Steam peeling has a higher influence on glycoalkaloid losses compared to that on phenolics. The highest amounts of phenolic compounds and glycoalkaloids were found in peeling byproduct. During processing, the amount of chlorogenic acid decreased, whereas the concentration of neochlorogenic acid increased due to isomerization. The impact of the results on potato processing technology is discussed.