Form 11 and PF Enrollment
At the time of joining, you should have collected Form 11, which declares that the employee is not an existing member of PF. Now, you can register him and start contributing to PF. This should not be done with a retrospective date but from the current month only.
Employee Declaration
To be on the safer side, you can collect a letter from the employee stating that he had declined to become a member of PF when he joined, but realizing the benefits associated with the schemes, he would like to get enrolled from this month. This declaration is not to be sent to the PF office, but it can be put in his personal file only. If you had not collected Form 11 earlier, you should collect it now.