This study highlights the diversity and complexity of traditional Kampo ointments in terms of chemical composition and, to a lesser extent, biological activity. Preparation temperature and ingredient origin markedly shaped the metabolite profiles, affecting both the formation of new lipophilic compounds and the degradation of healing-related metabolites. Higher heating temperatures and longer extraction times promoted the formation of modified lipid compounds and the loss of bioactive metabolites, such as tocopherols and sterols. Meanwhile, the botanical origin of Angelica acutiloba affected the quantity of glycosylated terpenoids associated with wound healing. Complete formulas were found to reduce keratinocyte migration in an in vitro monolayer model. Targeted metabolomics suggested a loss of vitamin E-like hydroquinone lipids in Shiunkō and the presence of an esterified diterpene in Shinsen taitsukō as possible contributors. The direct clinical relevance of these observations remains uncertain. These results emphasise the need for in-depth investigations into crude drug oily extractions, which are still underexplored. Research into traditional Kampo ointments could benefit from a more integrated approach that combines metabolomics with innovative biological models, in order to better elucidate their therapeutic applications in wound care.