The aromatic complexity of craft beers, together with some particular practices (use of small vessels, dry hopping, etc.), can cause more oxidation associated with pre-maturated colloidal instability, Madeira off-flavors, bitterness decrease, and aroma loss. As bottle refermentation is widely used in Belgian craft beers, the aim of the present work is to assess how this practice might impact their flavor. In fresh beers, key flavors were evidenced by four complementary techniques: short-chain fatty acids determination, esters analysis, XAD-2 extract olfactometry, and overall sensory analysis. In almost all of the fresh beers, isovaleric acid was the sole fatty acid found above its sensory threshold. Selected samples were further analyzed through natural aging at 20 °C. The presence of yeast in the bottle minimized the trans-2-nonenal released from Schiff bases and proved less deleterious than suggested by previous studies with regard to fatty acid release and ester decrease through aging. Furthermore, according to the yeast species selected, some interesting terpenols and phenols were produced from glucosides during storage.