The chartered architect programme will assess candidates' project management, decision making and communications skills, alongside technical systems integration and interoperability skills.
The certificate, which is expected to become available in the next 12 months, is geared towards high-flying IT professionals with business skills.
"We compare the certificate to a PhD where a candidate has to defend a thesis," said Ram Dhaliwal, training and certification manager at Microsoft.
Candidates will be expected to present a written submission to a board of technical experts and will be cross-examined on their work. They will work with mentors from Microsoft or other organisations during their assessment.
The chartered architect programme will require candidates to have a broad range of IT knowledge, and will have a Microsoft content of only 25%.
Microsoft said it was developing the programme following feedback from IT professionals who wanted to go a stage further than the organisation's existing Microsoft certified systems engineer qualifications.
"There will be a lot of individuals out there who have reached the point where they have the experience and who want to be tested at the next level," said Dhaliwal.
"For an organisation to have people with top level architecture skills that have been tested in front of their peers is quite powerful," he said.
Microsoft estimated that between 150 and 200 IT professionals in the UK will have sufficient experience and skills to take the certificate.