Melanin pigments are central to colors and patterns in modern vertebrate integuments, which inform upon ecological and behavioral strategies like crypsis, aposematism, and sociosexual selection. Over the last decade, melanin has emerged as a valuable tool for predicting color in exceptionally preserved fossil feathers and subsequent testing of paleobiological hypotheses in long-extinct dinosaurs and birds. Yet much remains to be learned about melanin stability, diagenetic alterations to melanin chemistry, and their implications for “paleocolor reconstruction.” Pressure–temperature maturation experiments with modern feathers offer a way to examine these topics but have mostly been conducted in closed-system capsules or open-system aluminum foil. Both methods have operational limitations and do not consider the filtering effect of porous sediment matrices on thermally labile chemical groups versus stable ones during natural fossilization. We use sediment-encased maturation to resolve this issue and demonstrate replication of organic preservation of melanin highly comparable to compression fossils. Our experiments, coupled with time-of-flight secondary ion mass spectrometry, show predictable volatilization of N/S-bearing molecules and increased melanin cross-linking with elevated temperatures. We also suggest that eumelanin is more stable compared with pheomelanin at higher temperatures, explaining why eumelanic colors (black, dark brown, iridescent) are better preserved in fossils than pheomelanic ones (reddish brown). Furthermore, we propose that proteins preferentially undergo hydrolysis more so than forming N-heterocycles in selectively open systems analogous to natural matrices. Thus, we conclude that melanin pigments and not diagenetically altered protein remnants are the key players in promoting fossilization of soft tissues like feathers.