Keith Brown said there was an “undeniable mandate” for an IndyRef2, with a majority of MSPs in Holyrood backing such a vote and that momentum was building behind the independence campaign.
But pro-Union campaigners warned that another referendum was “the last thing” Scotland needs as the UK continues to grapple with Brexit.
“There is no doubt that independence is coming – and Scotland will soon get to make that choice,” Mr Brown said ahead of conference.
“We have an undeniable mandate for a referendum, we have a majority in the Scottish Parliament and we have momentum on our side – with support continuing to grow in favour of taking our future into our own hands.
“In a democracy, no politician should stand in the way of the people. Scotland must have the chance to choose a better future as a matter of democratic necessity.
“We have seen hundreds of thousands taking to the streets, making clear that Scotland’s voice will be heard.
“And while Westminster politics are well and truly broken, more and more people are convinced that Scotland should grasp the opportunity to become an independent country.
“Though the Tories will always try to hold us back, the unstoppable energy of our movement will ensure we keep moving Scotland forward to independence.”
The opening day of the SNP conference is expected to see an attempt to force officials to add a debate on an alternative route to IndyRef2 to the agenda.
Senior councillor Chris McEleny and MP Angus MacNeil, who are behind the plan, believe it is “vital” the party considers what to do if the UK Government refuses permission for a vote.
Mr MacNeil said he felt the party had been engaging in “too much talk about the wrong referendum”, prioritising a drive for a second Brexit vote over a second independence referendum.
He and Mr McEleny want the SNP to declare that if it wins a pro-independence majority at the next Westminster or Holyrood election, it will have earned a mandate to start talks on exiting the UK.
The attempt to change the conference agenda will go ahead despite Nicola Sturgeon openly dismissing the idea, stressing there is no “short cut” to winning independence.
Pamela Nash, chief executive of Scotland in Union, said: “The very last thing that Scotland needs is a divisive and unwanted second independence referendum next year.
“The Brexit turmoil is causing deep divisions and economic uncertainty, and a referendum on leaving the UK would cause catastrophic upheaval.
She continued: “Nationalist politicians need to start listening to the people of Scotland. Barely a quarter back another referendum before 2021, and support for remaining in the UK has risen to 59 per cent. Scotland said no to separation in 2014 and we meant it.”