Things certainly improved for my DNephew in year 7 - Dsis was at her wit's end in the last two years of primary. There was a very toxic clique of boys (and parents!) who had all been friends since nursery. If your face didn't fit (no good at football, not deemed 'cool' or 'alpha' enough by the kids or their parents to be invited on playdates, even if you'd invited their kids to yours) you were - at best- excluded, or - at worst- picked on and victimised. The school tried very hard to support DNephew and the other boys in his class who didn't 'fit', but it was hard changing such a deep-rooted dynamic and one that essentially suited the families involved (they also dominated the PTA, but that's another story!). If one boy was called out on his shitty behaviour, all the other boys closed ranks and blamed the victim (as did the parents). Nightmare for the school to sort out, and a nightmare for Dsis and poor Dnephew too (and for me, as I picked him up from school a couple of times a week, often with him in tears).
Fast forward a year and it's a completely different picture. DNephew is transformed. Confident, happy, loads of friends who like him because he's funny, kind and smart - not because he's 'cool' and takes the piss out of the nicer kids to boost his popularity.
The toxic clique from his primary are floundering. Yes, they were deemed 'cool' in the first term, and a lot of the kids from other schools wanted to be friends with them initially (much to Dsis's dismay), but the group has started to fall apart as the kids from other feeder schools realise how mean these boys can be. The worst behaved in the group have resorted to more extreme and attention-seeking behaviour to keep their alpha status, which has seriously backfired on them. The school comes down on this behaviour like a ton of bricks - far more so than at primary, and the school won't put up with any crap or interference from the parents either. The more sensible kids in the year (thankfully the vast majority) have started to distance themselves, as they don't want to get into trouble, too.
Also, play-dates are seen as passe at secondary, so friendships often shift dramatically. Parents can't manipulate their child's popularity and friendship groups as much. The kids are finally left alone to make their own choices (good or bad!), rather than than having to be best-friends with the offspring of Mummy and Daddy's drinking buddies. Some of the parental friendships have floundered too, as they inevitably blame each other's kids when their own gets into trouble.
Try not to worry, OP. Encourage your Dd to join as many lunchtime clubs as possible, and gather as wide a pool of friends as she can - not the 'cool' kids, but the ones who seem happy in their own skin. Talk to her about the dangers of getting sucked into smaller, more exclusive groups - they might see themselves as the 'cool' kids, but are more often than not the most insecure, and more prone to bullying behaviour as they vie for position as 'top-dog'.
The change won't happen overnight, and things might feel worse before they get better if she drifts back to her old group in the first few weeks for security. But widening her group of friends is key, and if she's on what'sapp (which they shouldn't be at 11, but they all seem to be doing it anyway) keep a close eye on things. You might pick up on subtle signs of bullying/excluding behaviour in a group chat before your Dd even realises anything is wrong, and you can talk to her about how she should handle things.
My Ds is starting reception soon. Part of me is dreading it after seeing what Dsis had to put up with (if I hadn't witnessed some of it myself, I'd never have believed how manipulative and badly behaved some parents can be). Or perhaps they were just unlucky.
One last thing: after having their social lives engineered for so long, the more toxic 'popular' primary kids seem to struggle at secondary because they simply haven't developed the social skills to make themselves personable. DNephew knows how to make people like him, rather than be afraid of him. I'm sure your Dd will be the same.
Good luck!