The decision was made after new information about the Aberdeen Donside MSP was brought to party chiefs in the last 24 hours.
A spokesman for the party said: "Following new information being received by the SNP over the course of the last 24 hours relating to the behaviour of Mark McDonald, he has been suspended from both the parliamentary group and the party while further investigation takes place.
"In the interests of due process and appropriate confidentiality no further comment will be made."
The suspension comes 12 days after Mr McDonald stepped down as Childcare and Early Years Minister, admitting to a separate incident of “inappropriate” behaviour where he had sent a woman a text referring to a "sex act”.
The married father of two said at the time: “Some of my previous actions have been considered to be inappropriate - where I have believed myself to have been merely humorous or attempting to be friendly, my behaviour might have made others uncomfortable or led them to question my intentions."
Earlier this week before the latest allegations, he said that he was "determined" to change.
He said: “I have been offered support through the SNP to help me understand more about the way I behaved, the impact it had upon others and how I can work to ensure my behaviour does change. I have accepted that offer of support."