The organisation also warned both sides in the debate about Scottish independence that they would need to make a more compelling small business case to win the support of firms in the referendum set for September.
The Federations's Scottish policy convenor Andy Willox noted confidence had increased recently amid signs the economic outlook has improved.
"With more small businesses turning a profit, more planning to invest and more preparing to hire, the signs are that we're laying the foundations for a sustainable recovery," he said.
But, Mr Willox cautioned: "The recovery isn't uniform or guaranteed - certain sectors and certain areas are finding it much harder than others. We need banks to back our investment plans, public bodies to give smaller businesses a fair crack of the whip when bidding for public work and urgent action on overheads like utility prices."
He added: "The referendum on Scotland's future will present our small enterprises with a significant choice. The FSB, however, is concerned that we haven't yet seen a compelling small business case compiled by either side, with debate fluctuating between the macro-economic and the emotional." Mr Willox said both sides needed to detail what their preferred option would mean for small firms.