Thymelaceaous trees are prized for accumulating fragrant resins composed of hundreds of secondary metabolites in their woody tissues. Slow growth and increasing consumer demand have stretched natural sources of agarwood trees to being endangered and alternative production modes, including silviculture and tissue culture, are currently being investigated. Dedifferentiated tissue culture of agarwood trees provide a means of cell propagation independent of environmental context. However, secondary metabolite accumulation as found in fragrant resins, occurs largely in response to wounding. Here, we investigated the application of metal-organic frameworks (MOFs) as potential elicitors of secondary metabolite formation in Aquilaria crassna tissue culture samples. Callus cultures were exposed to five commercially available MOFs: UiO-67, MOF-808, HKUST-1, ZIF-67, and MOF-74, and ethanol extracts were used to quantify secondary metabolite accumulation compared to untreated cultures. Samples that were exposed to Zr-based MOFs exhibited similar metabolite production profiles, (trans-2-Carboxy-cyclo-hexyl)-acetic acid was reduced in the presence of all MOFs, the Cu-containing HKUST-1 MOF increased palmitic acid levels, and MOF-808 and ZIF-67 were found to elicit the highest accumulation of secondary metabolites with potential fragrance applications. These results demonstrate the possibility of eliciting secondary metabolites from dedifferentiated agarwood tree cell culture and may provide an alternative means of sourcing fragrant specialty chemicals from these plants.