Senior figures got the party's campaign under way by claiming the SNP is now fundamentally unattractive on the EU, while the Tories and Ukip could pull Britain out, damaging jobs and the economy.
George Lyon, the party's only MEP in Scotland, said: "We're giving people a very stark choice.
"Ukip and the Tories clearly want to walk out through the exit door, the SNP puts our place in Europe under threat through their independence plan, and Labour, they're split on Europe and as we saw they will hardly lift a finger to defend our place in the EU."
He was joined by Scottish Secretary Alistair Carmichael and Scottish party leader Willie Rennie to formally start his campaign for re-election.
The trio chose to promote their cause during a visit to a high-end whisky bottling plant on the edge of Edinburgh.
Mr Lyon focused the campaign message in response to the looming independence referendum on September 18.
Sending another SNP MEP to Brussels would not help Scotland maintain its level of support after independence, he claimed.
And he questioned claims in the Scottish Government's White Paper on independence which suggest full EU statehood can be achieved within 18 months of a "yes" vote.
"I believe the Scottish referendum and a vote for independence is indeed the first and biggest threat to our relationship with the EU," he said.
Asked if the SNP could keep the UK's current budget rebate, he said: "There's not a chance in hell.
"If you see how difficult it is in the negotiations, and I was involved in this for 17 months as part of the 12 MEPs that were nominated to do the negotiation with the other countries on the overall budget, and the UK permanent rebate is under attack at every single stage of the game.
"The idea that another small, independent country would come along and renegotiate this is fanciful in the extreme."
Mr Carmichael, the Lib Dem MP for Shetland and Orkney, said the SNP is now compromised on Europe.
"In the past the SNP have very much been in competition for the vote with ourselves," he said.
"Since they allowed their obsession with independence to take front and centre stage, they have diminished their own European credentials."
He added: "If you are genuinely a pro-European voter in Scotland then the SNP is now a fundamentally unattractive proposition for you."
Mr Rennie, MSP for Mid Scotland and Fife, said Mr Lyon is the most effective MEP in Britain.
"You've got a choice, you can have somebody of George's calibre who understands the budget process inside out, who understands the European Union, or you can have another nationalist banging the drum for independence," he said.
Of Scotland's six MEPs, the SNP and Labour both have two, while the Lib Dems and Conservatives have one each.
But with the Lib Dems having suffered a decline in support since the last European elections in 2009, there has been speculation that they might lose their only Scottish MEP in the upcoming ballot.
Labour and the SNP launched their European campaigns last week.
Labour leader Johann Lamont said the campaign should not be seen as an extension of the referendum campaign, while First Minister Alex Salmond said that Westminster representation in the European Union had ''let Scotland down time and time again''.
The election will be held on Thursday May 22.