My 3 month old has started to roll onto his tummy in his sleep and will cry if he gets stuck or frustrated. I go in and flip him back to his back and resettle him but within 20 minutes is rolling over in his cot again. I haven’t seen him roll back to his back during play time yet but I have seen him roll back on the monitor when he’s frustrated. Not sure if I should leave him or roll flip him and have him unsettled all night.

Now that your baby is rolling it is important that he is no longer wrapped or swaddled.
This includes using any swaddle suit that has his arms in.
Most babies will be rolling over by 4- 5 months - some earlier. This is very normal as babies grow & become stronger.
Many babies then prefer to sleep on their tummy.
This is not something that needs to be stopped. It is important to make his new environment as safe as possible.

Ensure that the cot mattress is firm & flat & there is nothing soft or loose in his cot
You can try to turn him back, but often, babies will just go back to their position of comfort, as you are finding.
Always continue to place baby on back to sleep.
Increasing tummy time when awake may also helpful.

Red Nose has the following information now that your baby is she starting to roll.

Give baby extra tummy time to play when awake and supervised as this helps baby to develop stronger neck and upper body muscles which in turn enables them to roll back over.
Make sure that baby is on a firm and well-fitting mattress that is flat (not tilted or elevated).
Make sure that baby’s face and head remains uncovered (do not use lambswool, doonas, pillows, cot bumpers or soft toys)

As babies grow and develop they become very active and learn to roll around the cot.
At this time, continue to put them on the back at the start of sleep time, but let them find their own position of comfort.
By this stage it is not necessary to wake during the night to turn baby over to the back position

Do not use any devices designed to keep baby in a particular sleep position.
https://rednose.org.au/article/what-do-we-do-now-that-a-baby-has-started-to-roll-over