The Bacc was introduced about a decade ago to offer a more rounded education.
Researchers at Cardiff University found students were 15% less likely to achieve a first or 2:1 degree.
The Welsh government said the Bacc will be more rigorous from September 2015, and it will address many findings in the report, which it commissioned.
The Welsh Bacc brings together traditional qualifications like GCSEs and A-levels with the Bacc "core," comprised of a range of modules including team enterprise activities, community participation and Wales' place in Europe and the world.
There are currently more than 78,000 learners registered on Welsh Baccalaureate courses studying at more than 250 schools and other institutions.
"Participation and progress are kind of connected," Prof Chris Taylor from Cardiff University, a co-author of the report, told BBC Radio Wales.
"On the one hand you'll find that students are significantly more likely to get into university with the Welsh Baccalaureate. Crucially, they are more likely to get into a leading Russell Group university, which is very good news.
"However that seems to come at the expense then in terms of their successes of degree outcomes.
"Although we find significant results, it does appear that students without the Welsh Baccalaureate are more likely to get a first or a 2:1."
He added: "The number of students who are not likely to get a good degree isn't as significantly as large as we first thought."
Prof Taylor said the Welsh Bacc's success in terms of getting students into university "far outweighs" the disadvantages found in terms of their results.
But he said: "We do make the recommendation that it could be more challenging. It could be more tailored to the particular needs of the students in terms of their choice of subjects at university they're going to study.
"We also recognise there needs to be greater support for the qualification because it has some added value.
"There are clearly some benefits to some students in terms of essay writing skills, in terms of time management and independent learning that most other qualifications don't offer.
"But it doesn't translate in terms of degree results and that may be because it's at the expense of subject knowledge which is missing."
"On the one hand it's a core qualification that every student should undertake and it provides a set of core skills that everybody like employers, labour markets and higher education universities can understand is there but at the same time it's got to be challenging, got to be tailored to the individual needs of students.
"That challenge is very difficult for sixth forms and FE colleges."
Last year, a study by the Welsh Institute of Social and Economic Research, Data and Methods (WISERD) also suggested undergraduates completing the Welsh Bacc fare less well at university than those who have not.
The Welsh government said the research by Cardiff University was commissioned to help with the development of the Welsh Bacc.
A spokesperson added: "Our independent review of qualifications addressed many of the findings in the WISERD report, and we are already taking action to deliver the review's recommendations regarding the Welsh Baccalaureate.
"As a result, we are working towards delivering a more rigorous Welsh Baccalaureate to be taught from September 2015.
"This will provide further assurance to higher education institutions about the ability of Welsh Baccalaureate learners and will help university admissions tutors make offers to prospective learners."
University students who studied the Welsh Baccalaureate are less likely to get higher degrees than those who did not, a report suggests.