إِنِّي أَنَا رَبُّكَ فَاخْلَعْ نَعْلَيْكَ ۖ إِنَّكَ بِالْوَادِ الْمُقَدَّسِ طُوًى (12)
(20:12) Lord; take off your shoes, *7 for you are in the sacred vally of Tuwa. *8
*7) Probably, it is because of this that the Jews do not say their prayers with their shoes on. The Holy Prophet, however, removed this misunderstanding, saying, "Act in contrast to the practice of the Jews who do not say their prayers with their shoes or leather socks on." (Abu Da'ud). It does not, however, mean that one must say one's prayers with the shoes on, but it is merely to make it lawful to say prayers with shoes on. This is confirmed by another tradition, related by Abu Da'ud from `Amar bin `As, that he had seen the Holy Prophet saying his prayer both with and without the shoes.
There are other traditions also to this effect but it should also be kept in mind that there were no carpets, mats, etc. in the mosques in those days, not even in the Holy Prophet's Mosque. Therefore it would be improper to go with shoes on into the mosques of today which have carpets, mats, etc. However, one may say one's prayer on grassy plots or open ground with shoes on.
*8) In general, the commentators are of the opinion that Tuwa was the name of the valley, but according to some it means, "The valley that had been made sacred for the time being. "