Its annual report says more schoolgirls are opting to take home economics rather than traditionally male-dominated subjects such as IT or design and technology.
Yet, when it comes to overall performance, the girls are still on top - consistently beating boys' achievements at key stage 3, GCSE and A-level.
Susan Lewis, chief inspector of schools in Wales, said many schools are encouraging boys and girls to choose the subjects they enjoy for GCSE in a bid to close the performance divide.
But the standards-raising tactic has been at the cost of letting pupils make more stereotypical choices. "Let's not be too politically correct here - girls choosing home economics is not a bad thing," said Ms Lewis. "I think it is important to allow pupils to follow the subjects they want to do."
But a spokesperson for the Equal Opportunities Commission in Wales said:
"Girls are not being given the type of careers advice, work-experience placements and training opportunities that would help them make genuine career choices and get jobs that attract higher pay."
Post-16, females make up more than 70 per cent of exam entries in English, Welsh, Welsh second language, foreign languages, home economics, religious studies, and sociology. The also dominate art and drama.
In FE colleges inspected by Estyn in 2004-5, only 3 per cent of the total enrolments in construction were female, and 7 per cent in engineering.
Estyn's annual report suggests girls may prefer subjects where they can be emotional as well as creative.