I'm taking my 9 year old daughter to Paris, Rome and London in September. Looking for recommendations on things to do and see that are off the beaten track. TIA

I would suggest checking out the Rick Steves’ Europe Group.

We loved the little area of Trastevere in Rome we stayed in at an Airbnb. Small town cobbled street vibe but close enough to walk to all the sites.

I recommend the boat trip in London from Little Venice to Camden Market followed by lunch and shopping at the market.
https://www.londonwaterbus.com
LONDONWATERBUS.COM
LONDON WATERBUS COMPANY

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We are doing a bakery tour In Paris, making baguettes and pastries.
Bike tour at Versailles , it’s mostly all flat and takes you into the village market for a spot of shopping .
Don’t forget the catacombs in Paris. Sufficiently macabre for a youngster .
High tea in London at Langham hotel.
There is a company that organizes “ mudlarking “ in London on the Thames. But pricer because you need to buy a permit to do it. But basically you trawl the coastline / river bank for treasures buried in the sand . Kids would be fascinated with the hunt. You can find you tube videos online. They find old bottles , coins, sometimes ancient Roman trinkets.

In Paris we went to a private Museum of Carnival Arts, Musee des Arts Forains I think
my kids loved it, got to try all kinds of old interactive games and even rides. The Louvre, Jardin Tuileries and Musee D'Orsay, as well as the Bersey and Montmartre were some of my kids favorite areas to explore. We have a strict 90 minute policy, that is the max time we spend in galleries or museums no matter what. Keeps all of us from feeling fatigued, and everyone looks ahead to find exhibits they really want to see, we enjoy those and even if we don't see an entire building full of art it does not matter. Then we would do something more kid focused afterwards.
In London we love some of the the further flung markets like Portobello or Camden, and like the Greenwich and Canary Wharf areas. So easy to get around by Tube there. I do have a soft spot for Covent Garden, the British Museum and V&A Museum. Many museums are free entry, so enjoy even a short stops.
Rome itself is like walking through an archeological site, would recommend a hop on and off tour bus to get your bearings. As an aside, some of the best quality and affordable food we had in Rome was the Mercato Central at the train station, like a fancy food court with local foods. Hot tip from a local, they were not wrong! I second Trastevere.
In all cities let yourself just wander, it's amazing what you will find. I have been to all 3 cities and the fun has always been getting away from the touristy areas, and finding some quieter streets to explore.

They are all huge cities. If you say exactly where you'll be staying and how long you'll be in each location, you'll get better responses. Off the beaten track might be 30 min from Victoria Station but 2 hrs from Wembley. If you only have 3 days in London, you'll want suggestions closer to where you're staying.

I took my daughter on a Fat Tire Bike Tour in Paris. She loved it. Way more fun than a bus.

In each city first get a free map from the underground stations of your hotel —- go on a double decker tour bus sit upstairs open deck — follow the route on your map — then snuggle area that looks fun and interesting the tbe next day get the underground / metro to it . So east to get around — get a day transit pass for each city which can be used on over ground buses and underground .
Have fun !

Disneyland in Paris

Fat Tire Bike Tours for sure!

What ever you end up doing, travel is so of the best life experience education you can give her.
If you get out of London there are some cool heritage open Air museum, here is one....https://www.wealddown.co.uk/ that all interactive, what people/staff dressed up in the era.
There is a few other open Air interactive museums, and the greater area. Very worth checking out.
WEALDDOWN.CO.UK
Explore The Weald & Downland Living Museum in Chichester

Stay on the surface. First time in Paris I took the Metro everywhere. Meh! Next time in Paris I was broke but had to wait 3 days for my flight. Had to walk everywhere. Fell in love with the place. Learned that if you take the underground/metro/subway you could be anywhere and you miss what's best about the place. By extension I now try to avoid freeways and drive on secondary routes. Much nicer.