Metastasis is responsible for the majority of cancer-related deaths. Tumour invasion and metastasis result from processes that include the proteolytic degradation of the extracellular matrix adjacent to the tumour. The matrix metalloproteinases (MMPs), particularly MMP-2 and MMP-9, have prognostic influence in human cancers after they cleave the main structural components of the basal membrane. These actions make MMPs an attractive target for cancer and metastasis studies. This study evaluated the inhibitory potency of extracts of Bauhinia ungulata L. (BU) on the gelatinolytic activity of MMP-2 and-9 and recognized the group of secondary compounds responsible for this property. The zymographic analysis of the BU stem revealed that the ethyl acetate partition (D) caused a higher inhibition of MMP-2 and MMP-9. The phytochemical study of D showed the presence of steroids, tannins, and coumarins and the significant presence of alkaloids and flavonoids. The phytochemical study of the fractions obtained through the column chromatography of partition D revealed a significant presence of flavonoids and alkaloids in the fractions that showed better inhibition of the gelatinolytic activity of MMPs. In conclusion, these results suggest that the stem fraction of BU has the potential to inhibit MMP-2 and MMP-9 and should be used in studies on the recognition of active biomolecules.