Once released into the environment, petroleum is exposed to biological and physical weathering processes which can lead to the formation and accumulation of highly recalcitrant polar compounds. These polar compounds are often challenging to analyse and can be present as an “unresolved complex mixture” (UCM) in total petroleum hydrocarbon (TPH) analyses and can be mistaken for natural organic matter. Existing research on UCMs comprised of polar compounds is limited, with a majority of the compounds remaining unidentified and their long-term persistence unknown. Here, we investigated the potential biodegradation of these recalcitrant polar compounds isolated from weathered diesel contaminant, and the changes in the microbial community composition associated with the biodegradation process. Microcosms were used to study the biodegradability of the polar compounds under various aerobic and anaerobic conditions and the results compared against the biodegradation of fresh diesel. Under all conditions tested, the majority of the polar UCM contaminant remained recalcitrant to biodegradation. The degradation was limited to the TPH portion of the polar UCM, which represented a minor fraction of the total polar UCM concentration. Changes in microbial community composition were observed under different redox conditions and in the presence of different contaminants. This work furthers the understanding of the biodegradation and long-term recalcitrance of polar compounds formed through weathering at contaminated legacy sites.