The 90-day clock begins on either the date of the action giving rise to the complaint, or the date that action comes to the attention of the employee, whatever is later. After the personal grievance has been raised, an employee has three years to bring it to the Employment Relations Authority (which is like a court but more informal).
It is possible to raise a personal grievance outside of the 90-day timeframe. However, it can be difficult. To do it, you will need either the consent of the employer, or the permission of the Employment Relations Authority. If there is no good reason for the delay, you may be unsuccessful.
There may be time limits on other complaint avenues as well. For example, civil court (which is when you need to go somewhere like the district court or the High Court for non-criminal-related matters) normally has a time limit of six years. The Privacy Commissioner and Human Rights Review Tribunal are not bound by a limitation period, but they may not accept a claim if it is made too late.
If something has gone wrong at work, contact a lawyer immediately. Employers can sometimes try to keep things calm until the 90-day timeframe has expired, so don't delay because things seem okay for the moment.
