Damaged cacao seeds are often unsuitable for the cocoa value chain due to compromised sensory and functional qualities caused by diseases during cultivation. Fermentation is crucial in enhancing the sensory and biochemical properties of cocoa beans – the resulting product after fermentation. The aim of this work was to evaluate the effects of spontaneous fermentation (SF) and fermentation-like incubation (FLI) on metabolomic profiles of damaged and healthy samples. SF was conducted using cacao seeds in wooden boxes for five days. Fresh and dried seeds, both healthy and damaged, underwent FLI in a solution of acetic acid (0.15 mol/L) and ethanol (5%) at 50°C for four days, with constant agitation. The beans were then dried to a moisture content of <8%. Metabolomic profiling was conducted using Nuclear Magnetic Resonance (NMR) and Gas Chromatography-Mass Spectrometry (GC-MS). Multivariate Statistical Analysis (MVA) was used to compare the treatments. FLI significantly altered the metabolomic profiles of damaged beans, reducing sucrose levels, indicating sugar breakdown during metabolic activities. In untreated dry seeds, sucrose levels remained high, suggesting preservation during drying. Leucine and tyrosine concentrations increased in treated samples, particularly in damaged beans, reflecting enhanced protein metabolism. Volatile compounds such as pyrazine, linked to cacao aroma, were abundant in both fermented and FLI samples, in similar levels for healthy and damaged beans. MVA revealed that FLI successfully replicated key biochemical effects of SF, demonstrating its potential to improve the quality of damaged cacao seeds. The preservation of key metabolites like amino acids and aroma compounds suggests that this method can enhance both the sensory and functional properties of cacao. FLI proved to be an effective alternative to SF, improving the quality of damaged cacao seeds and supporting their use in industrial processes, while contributing to a more sustainable cocoa production system.