Plant growth can be influenced by the application of triazole pesticides as these regulate physiological processes such as plant hormonal levels and enzyme activity. Homology modeling and molecular docking studies suggested that inhibition of ADP-glucose pyrophosphorylase activity in two trans-stereoisomers treatments hinders starch accumulation during the grain filling stage. A field experiment investigated the effects of metconazole racemate, cis-1R,5S-stereostereoisomer, and cis-1S,5R-stereoisomer application at the flowering stage on wheat grain ripening and yield. The concentrations of racemate and both cis-stereoisomers were detected in wheat plant and grain samples. Compared with the racemate, both cis-stereoisomers were more persistent in the matrices. Treatment with cis-1R,5S-stereoisomer decreased grain weight and yield of wheat by delaying chlorophyll degradation, increasing the ethylene content, and decreasing the level of abscisic acid. The germination of harvested seeds was adversely affected by racemate treatment as a result of gibberellin and abscisic acid metabolism regulation and the transcription of signaling-related genes. Therefore, cis-1S,5R-stereoisomer was recommended to be used as metconazole pesticide at the flowering stage. Display omitted •The stereoselectivity of metconazole on wheat grain development was evaluated.•metconazole cis-stereoisomers exhibited less inhibition on AGPase activity.•cis-1S,5R-metconazole is more recommended for wheat at flowering stage.