One of the focuses will be on the two trustees, Rabbi Mordechai Bamberger and his brother Solomon, and their handling of potential conflicts of interest and whether they fulfilled their duties under charity law.
The probe will also look into whether there has been any unauthorised or indirect private benefit or any financial loss incurred due to mismanagement or misconduct.
But the Commission stressed "the opening of an inquiry is not a finding of wrongdoing."
The M B Foundation, also known as the Mossad Horav Aryeh Halevy, operates in Bury and Israel.
Its last financial statement for the year ending in March 2020 says it paid out more than £830,000 in grants to support community projects, schools and yeshivot in a bid to advance Jewish education and faith and for poverty relief in the community.
The M B Foundation was approached for comment.
