In the present study, two Aspergillus species as biocontrol agents together with Chenopodium quinoa dry biomass were used to investigate their effects on histochemical features of mungbean plant inoculated with M. phaseolina. In a pot experiment, Aspergillus flavipes and Aspergillus versicolor were added either alone or together with 1%, 2%, and 3% dry biomass of quinoa (DBQ) to the pot soil already inoculated with M. phaseolina. After 4 weeks of sowing, root and lower‐stem sections of the mungbean plants were stained with ferric chloride, phloroglucinol‐HCl and Lugol's iodine to detect the presence of polyphenols, lignin, and starch granules, respectively, and observed under light microscope. Stem and root sections were also observed under scanning electron microscope (SEM) to reveal the effect of soil amendments on cell structures. The findings revealed that mungbean plant cross sections from all the treatments except positive control (only inoculated with M. phaseolina) showed very clear cell structures. In positive control, distorted, fragmented, and collapsed cell structures were observed. Moreover, M. phaseolina blocked vascular vessels in comparison to negative control where the cell structures were intact and normal in size. Plant sections from treatments with A. flavipes and A. versicolor alone or together with DBQ were without pathogen colonization, with normal cell structures and a high deposition of gel. The results suggested that the two Aspergillus spp. and C. quinoa induced defense responses in mungbean plants.