The cross-party campaign splashed £170,965 on preparing its 3500sqft HQ on Glasgow's Hope Street, and buying computers and other office equipment, its first accounts reveal.
The cost - equal to 10% of all Yes Scotland's declared donations - reflect its decision to move into an unfurnished basement with no internal dividing walls, forcing it to pay extra for the designers, materials and manpower to create an entire office suite from scratch.
The Hope Street address was meant to symbolise the Yes camp's upbeat mood. The refurbishment also created a drop-in area for voters to learn about independence and buy Yes goods.
But one insider said the lavish office was now regarded as a mistake, and blamed Yes Scotland getting carried away by an initial rush of money, leading to unnecessary spending, including the hiring of five highly-paid directors who have all since left.
In contrast, the pro-UK Better Together campaign moved into serviced offices a few blocks from Yes Scotland and spent £5000 on computers.
One source close to Yes Scotland said: "In a campaign, £100,000 is not a lot, but it's still money that could have been used somewhere else."
The Sunday Herald revealed last week that Yes Scotland had laid off the last two members of its original five-strong "top team" of directors appointed in September 2012, prompting claims the outfit was in meltdown.
Yes Scotland, which denies it has money problems, has also delayed publication of its donor income, despite chief executive Blair Jenkins promising financial transparency.
Better Together said the Hope Street HQ represented the financial recklessness typical of the Yes camp.
An insider said: "I'm sure the directors of Yes Scotland who have been sacked in recent weeks will take great comfort from the fact that they got to work in an expensively assembled office for a few months before the cash ran out."
A senior SNP member said the office spending "smacked of a vanity project".
Asked if the office was worth it, a Yes Scotland spokesman said: "The HQ, in terms of location, the services it provides and its role as the nerve centre for the Yes movement, matches the crucial importance of this campaign."