Speaking at a meeting for social enterprises and community interest companies in London last week, Dame Suzi Leather told leaders to "look for the right vehicle to pursue passion" when considering legal frameworks.
"Make sure that structure follows strategy, and not the other way around," she said. "Don't twist your aims and activities to fit the format you think will be easiest.
"A starting position where format dictates strategic direction is hardly a recipe for success."
Leather was speaking on the same day that the commission issued new guidance on trading arms or subsidiary companies.
Trustees, Trade and Tax: how charities may lawfully trade was published in response to a call from the Better Regulation Commission for more user-friendly guidance.
Leather said she hoped to explode the "big myth" that the commission did not approve of charitable trading or social enterprise: "We do recognise social enterprise as a source of benefit to the community, and aim to support its growth."