Cherished amber relics have undergone long-period burial environments carrying several ageing deterioration characteristics, such as crazing, discolouration, and decreased hardness, which makes amber artefacts fragile. Ageing is inevitable for amber exposed to air, emphasising the need for a suitable preservation environment based on the ageing mechanism. However, related research, specifically on the transformed compositions and structures of archaeological amber, has been limited due to complexities in deciphering the intricate components. In this research, attenuated total reflection Fourier transform infrared (ATR-FTIR), X-ray fluorescence (XRF), inductively coupled plasma optical emission spectroscopy (ICP-OES) and pyrolysis–gas chromatography/mass spectrometry (Py-GC/MS) were applied on geological and archaeological Baltic amber to find the ageing pathways. An untargeted metabolomics analysis developed for the linear modelling of molecular features data was utilised in combination with Py-GC/MS results, and statistically significant variations provided ten increased and ten decreased ageing markers. We propose an ageing mechanism for the succinite molecular structure, which involves oxidation of the polylabdanoid and hydrolysis of the esterification cross-link structure between succinic acid and labdanoid. Simultaneously, monoterpenes were released from the amber structure. Our untargeted Py-GC/MS metabolomics approach offers a groundbreaking and more systematic method for investigating the ageing mechanism of multi-component organic polymers in archaeological artefacts.