Speaking after a month in the role, Petra Wend said a merger was "off the cards", despite recent speculation that the Scottish Funding Council would welcome the move after it identified overlaps in the institutions' teaching offerings.
"The university would not have appointed a new principal if the governors thought that a merger would happen," she said. "Our ambition is to be sustainable and independent - that's environmental but also financial sustainability."
Professor Wend said that Queen Margaret, which has just 5,000 students, would recruit more postgraduates and international students to help pay off a £7 million debt incurred as a result of its move to a new campus outside Edinburgh.
She said that the campus was a significant asset, adding that other universities were struggling to find the money to build in the recession.
Since joining the institution, Professor Wend has moved to resolve problems in its drama department.
A row broke out earlier this year over an attempt to redesign its undergraduate degree programme, prompting several former members of staff to write an open letter to the Quality Assurance Agency Scotland criticising the lack of practical tuition on the proposed course.
Professor Wend has written a joint letter to the SFC with Joan Stringer, principal of Edinburgh Napier University, detailing plans to deliver drama across the two institutions.
So while a merger may be out of the equation, collaboration is not. Professor Wend said that their joint drama proposals had a "highly practical" element, as well as a "community focus". She is now conducting a review of all Queen Margaret courses. She said that under her stewardship, the university will focus on three areas: health, the creative industries and business.
"I want to converge academic excellence with financial sustainability," Professor Wend said.
On wider issues affecting Scottish higher education, she expressed concern over the proposed changes to teaching funding outlined by the SFC earlier this month, which she said would have a disproportionate impact on Queen Margaret.
The plans, which are under consultation until December, propose a rejig of funding for specific disciplines that could see more money going to Scotland's ancient universities and less to its new institutions, including Queen Margaret.
Professor Wend also set out her views on fees, which she opposes.
"Being German, it was written in the German constitution that education has to be free. A very personal element of me says no," she said.
Joined-up thinking: Glasgow plans college route
The University of Glasgow is to adopt a collegiate structure, merging its nine academic faculties into four colleges by August 2010.
A consultation has already begun, with recommendations due to go before the university's court in December.
A Glasgow spokesman said it would give it "greater agility in responding to opportunities, reduce bureaucracy and remove the duplication of administrative effort".
Glasgow is not the first to adopt such a structure: the universities of Exeter and Leicester are also reorganising into colleges, and the University of Birmingham did so last year.