Both immanently high active iron contents and increased root ferrous uptake in response to low iron stress contribute to the iron deficiency tolerance in Malus xiaojinensis.

•The immanent active iron contents in M. xiaojinensis are higher than M. baccata.•Root ferrous uptake was activated after iron starvation in M. xiaojinensis.•In M. baccata iron relocalization started rapidly in response to low-iron stress.•Iron relocalization started after 5 days of low-iron treatment in M. xiaojinensis.