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Simple Summary: Surprisingly, there is little research on the antimicrobial activity of stingless bee propolis on disease-causing microorganisms in animals. The present work demonstrates the effect of propolis from two native Mexican bees, Scaptotrigona mexicana and Tetragonisca angustula, on the yeast Malassezia pachydermatis, the main agent of canine otitis externa, and its damage to the cellular structure. The chemical analysis showed that the most abundant components are some sesquiterpenes. The antifungal activity of the propolis was evaluated using both strains isolated from clinical cases and a reference strain. Both types of propolis inhibited all Malassezia pachidermatis strains. Cell damage was assessed by fluorescence microscopy with calcofluor white, which specifically stains the fungal cell wall, and propidium iodide, which has the ability to stain the interior of the cell, only if the cell wall or membrane has been damaged. The propidium iodide staining of the yeasts treated with both types of propolis revealed the penetration of this marker, which suggests the destruction of the cell wall and plasma membrane of the fungi. These results suggest that these types of propolis could be used as alternative treatments for canine external otitis. This seems to be the first scientific report that has demonstrated structural damage in Malassezia pachydermatis by Mexican stingless bee propolis. This work describes the antimycotic activity of propolis from the stingless bees Scaptotrigona mexicana and Tetragonisca angustula, collected from two Mexican regions (Veracruz and Chiapas, respectively), against three clinical isolates and the reference strain ATCC 14522 of Malassezia pachydermatis, the causative agent of canine otitis. The chemical components of the ethanolic extracts of propolis were determined by gas chromatography coupled with mass spectrometry (GC-MS), and sesquiterpenes were the predominant compounds. The antimycotic activity was evaluated by plate microdilution. The induced changes in the yeasts were evaluated by fluorescence microscopy and staining with calcofluor white and propidium iodide. The minimum inhibitory concentration (MIC) was 7.11 mg/mL, and the minimum fungicidal concentration was 21.33 mg/mL for both extracts. The EPPs of Scaptotrigona mexicana and Tetragonisca angustula caused substantial damage to yeast morphology, where the propidium iodide staining of the yeasts treated with both EEPs revealed the penetration of this marker, which indicates the destruction of the cell wall and plasma membrane of the fungi. This result suggests that these types of propolis could be used as alternative treatments for canine external otitis. To the best of our knowledge, this seems to be the first scientific report that has demonstrated structural damage in Malassezia pachydermatis by Mexican stingless bee propolis. [ABSTRACT FROM AUTHOR]