The reaction of 2-oxo-N-arylpropanehydrazonoyl chlorides 3a-e with 3-methyl-2-benzofurancarboxylic acid hydrazide (7) furnished N-(aryl)propanehydrazonoyl chlorides 8a-e. X-Ray of 8c revealed the (1Z,2E) configuration of structure 8. Nucleophilic substitution reaction of 8a or 8d with piperidine resulted in the formation of 1-(piperidin-1-yl)-N(2)-arylamidrazones 9a, b. The X-ray diffraction of 9b showed its (1E,2E) configuration and it confirmed the stereoselectivity of the latter reaction. (1E,2Z,3E)-1-(Piperidin-1-yl)-1-(arylhydrazono)-2-[(3-methylbenzofuran-2-oyl)hydrazono]-4-arylbut-3-enes 11 were synthesized in stereoselective reaction from 8 or alternatively from 9. X-ray analysis of 11b showed a conversion of configuration respect to 8d or 9b. X-Ray analysis of 9b and 11b revealed the role of hydrogen interactions in the stereochemistry of their solid state structure. The in vitro antimicrobial activity of the newly synthesized compounds demonstrated an excellent growth inhibition of compounds 9 and 11 against clinically isolated strains of human fungal pathogens and exhibited a significant potency against gram-positive bacteria. Griseofulvin and Amoxicilline were used as references for antifungal and antibacterial screening. The effect of most potent antifungal compound 9b on morphological features of Aspergillus fumigatus and Candida albicans using image analyzer was studied. Furthermore, the effect of 9b on the ultra-structures of the latter fungi was occurred by transmission electron microscope.