High school pupils are now required to wear face masks between classes.
From Monday morning, pupils over the age of 12 are expected to wear coverings in areas where physical distancing is not possible, like corridors and communal areas.
All children aged five and over are also required to cover their faces on school transport, such as buses and trains, in line with the current guidelines for public transport.
There will be no requirement to wear face coverings in classrooms where distancing measures are in place.
The Scottish Government guidance also states staff and students can continue to wear face coverings in all settings voluntarily if they wish.
Young people returned to schools earlier in August with no requirements for physical distancing between younger pupils, and no rules around face coverings.
However last week education secretary John Swinney announced the change in guidelines. He said: “We said that our guidance would be kept under constant review and, following updated scientific and public health advice and the experience of schools reopening, we are making changes that will apply from August 31.
“There is increasing evidence that face coverings can provide some protection for the wearer as well as those around them.
“We also know that some pupils have found it very difficult to physically distance when moving around school, which could increase the risk of transmission of the virus.
“And on school transport, as on public transport, there can be mixing between different age groups.”
Some pupils will be exempt from wearing a face covering, whilst those who do not want to wear one are not to be excluded from school.
The deputy FM added: “Alongside this change to the wearing of face coverings, we need to reinforce the importance of maintaining high standards of cleaning, personal hand and respiratory hygiene and physical distancing, where possible.
“In situations where there is a local cluster, use of face coverings throughout the day may be required.
“The position will be kept under review to ensure that our approach remains commensurate with the evidence and the levels of transmission in Scotland.”