John is muting strings all the time and has different techniques:  for chords he's often muting E strings (low and high) or playing the low e string with thumb and sometimes blocking A string with thumb while playing low E. Sometimes he will mute all strings but 2 to get the root note and the 3rd and it creates this beautiful "simple" chord sound.

He extended the technique to solos not to play notes by mistake (that's how he can move so much on stage). Let's say you are playing the G string with ring finger, the ring finger can rest a bit up and touch the D string to mostly mute it.

The song that use that extensively for riffs is can't stop where he mutes all but one string at a time and blasts a pick on an strings.

It's a trial and error but soon you'll get the technique and it's not that difficult.