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The purpose of this work is to study the evolution, over three selected harvests, of phenolic compounds and colour stability of red wines produced in the north of Portugal by means of two wine-making processes (conventional maceration/fermentation and fermentation after initial carbonic maceration), with and without the use of four different fining agents (polyvinylpolypyrrolidine, gelatine, egg albumin, and casein). In general, it was observed that wines obtained by conventional maceration/fermentation (PO) present the highest colour intensity and polyphenolic content (total and monomeric anthocyanins, flavan-3-ol monomers and polymers), and the lowest orange–red hue, immediately following vinification. Nevertheless, carbonic maceration (CM) afforded wines with most stability in colour density, for 26 months’ storage. Different evolutions of anthocyanins and of flavan-3-ol monomers (catechins) and polymers (procyanidins) in PO and CM protocols during storage were observed. Decrease of anthocyanins and flavan-3-ol dimmers were, in general, more remarkable in PO wines. Monomers and trimers underwent a rise, especially in CM wines. Wines treated with fining agents tended to have somewhat lower anthocyanins levels, and especially in the case of PVPP, less intense colouration than untreated wines. Principal component analysis (PCA) revealed that catechins and some procyanidins are mainly responsible for the separation and evolution of wines during storage according polyphenolic composition. Partial least squares (PLS) regression models confirm that colour density in wines from PO and CM protocols explains a high proportion of the variance in hue, chemical age, IFC and anthocyanins and a prediction model has been built.