Impressed by the work done around the club since the allegations emerged last year, the England and Wales Cricket Board announced the conditional restoration of hosting rights on Friday afternoon.
Rafiq's claims of racism and bullying saw a culling of staff around the club, and under new chair Lord Kamlesh Patel, Yorkshire have strived for improved inclusivity and diversity.
As a result, the ECB restored hosting rights but only with the agreement that two conditions are met.
The governing body says Yorkshire must "resolve the issues relating to rules changes and decisions at the club which have been subject to procedural flaws".
This demand follows the late-notice cancellation of an extraordinary general meeting of members due to take place last week, owing to a failure by the previous leadership to file rule changes with the Financial Conduct Authority.
The ECB also wants "amendments to club rules relating to the appointment and operation of the board, including removal of Graves Trust powers" before any matches are hosted.
Members had been due to vote on changes to club rules which would allow up to eight non-members to join Yorkshire's board as independent non-executive directors.
Following the announcement, Rafiq welcomed the news and stated that he believes the ECB have made the "correct decision".
Rafiq said: "This is the correct decision by the ECB - under Lord Patel the club has shown a real willingness to change and has already come a long way.
"His leadership has earned the club another chance, but the reforms must continue and we must see real change."
The first matches to be hosted back at Headingley will be the third Test against New Zealand in June and July's one-day international against South Africa, as long as the ECB's conditions have been met by the end of March.