The SNP leader has been a steadfast defender of the deal, which brought the Greens co-leaders into Government and shored up the pro-independence majority in Holyrood.
The arrangement allows the party to differ on certain policy aspects, but brought forward shared commitments like highly protected marine areas, which were sent back to the drawing board after an outcry by fishing communities.
Some senior figures within the SNP, most vocally former minister Fergus Ewing, and others within the Scottish independence movement have criticised the agreement.
But Mr Yousaf has insisted that the SNP continues to support the Bute House Agreement with the rival party, pointing to his vocal backing of the arrangement during the SNP leadership contest.
Speaking on a visit to Glasgow’s Riverside Museum, the First Minister said: “We’ve already had a vote and 95% of our membership backed it.
“We’ve just had a leadership election, of course, in which the Green deal was a central issue, and I’m pleased that I was elected as leader of the SNP.”
Mr Yousaf – who has spent the summer campaigning in different parts of the country – said he has “knocked a lot of doors” and rarely has the deal between the two parties been brought up.
Read more: Harvie defends Bute House Agreement
Asked if he believes his argument would be backed by the membership, he said: “Yes, absolutely.”
Mr Ewing has been the loudest voice against the deal, describing the Greens as “wine bar revolutionaries” and arguing that Scottish Government policy had been pulled to the left by the agreement – signed under Nicola Sturgeon.
Many of the polices under fire, such as the deposit return scheme, have been SNP commitments for many years.
Both candidates who faced Mr Yousaf in the recent leadership contest were also sceptical of the pairing, with former finance secretary Kate Forbes saying recently the party should “check in” with members on the deal.
Senior SNP figures have repeatedly rejected such an idea.
Meanwhile, the party’s new chief executive took up the post on Monday.
Murray Foote was previously the SNP’s head of communications, before he quit earlier this year after being given incorrect membership numbers to brief the press by Peter Murrell – Nicola Sturgeon’s husband and the man he replaced in the top job.