When does the 90-day restoration period actually start?

The 90 days run from the day you actually lost status. What trips people up is that the day you lost status is not always the day your permit expired.
If you did not apply for anything before your permit expired
You lost status on the expiry date, and the 90 days runs from there.
If you applied to extend before your permit expired and were refused later
This is the one that confuses everybody. Applying before your status runs out puts you on maintained status, and IRCC's instructions say your "period of authorized stay as a temporary resident is extended by law until a decision is made."
So you did not lose status when the permit expired. You held it the entire time the application sat there. The same page says you are "considered in status until the day the decision is made on their application", and that "the 90-day restoration period under section R182 begins on the date of refusal."
The date to count from is printed on your refusal letter. Not your permit expiry, and not the day the letter landed in your inbox.
If you were already out of status, applied for restoration, and that was refused
There is no second 90 days. The window is attached to the day you lost status, and a refused restoration does not reset it. If the original window has closed, restoration is no longer available to you, whatever the second letter says.
Leaving Canada ends both
Maintained status "ends when they leave Canada." A restoration application requires you to remain in Canada until a decision is made, so leaving while it is pending means it gets refused and the fee is not returned.
There is also a trap on re-entry. If you leave while an extension is pending, you cannot resume working or studying when you come back until the new permit has actually been issued.
What you cannot do while a restoration is pending
You cannot work or study. Not reduced hours, not for the same employer. The instructions say an applicant "may not continue to work or attend school until their restoration application has been approved", and the authorisation itself has to be issued on top of the approval. If the work permit side is the part that is not ready, there is a separate route. You can restore your status as a visitor instead, which holds your status without the work authorisation attached to it.
Sources
Temporary residents: Maintained status during processing, IRCC program delivery instructions, modified 28 May 2025.
Restoration of temporary resident status, IRCC program delivery instructions, modified 1 May 2026.
If you ended up here because your post-graduation work permit window closed rather than because of a refusal, that one has its own answer.
If your clock started with a refused bridging permit, it is worth understanding why that refusal happened before deciding what to do next: https://www.nextmovepath.com/community/why-was-my-bowp-refused-when-bulletin-699-says-i-do-not-need-an-aor/
If your own dates do not fit cleanly into one of those three, what settles it is the date on your permit read together with the date on your refusal letter. Post both, and we will work it through.