A tree grew through this pen. Let that sink in. Not a sapling, not a branch, a full-on, established tree, right up through the dog run like it owned the place. That's either a sign of extreme neglect or a testament to the kind of stubborn, patient planning that makes for a surprisingly solid chicken coop. I'm leaning toward the latter, mostly because the person who posted this already knows they have raccoons and bobcats. That's not a beginner thinking this will be easy. That's someone who has looked at the local predator lineup and said, "Fine, I'll build a fortress around a tree."
And honestly? That's exactly the energy you want. The tree is not a problem. It's a perch, a shade structure, and a built-in climbing deterrent for anything that isn't a chicken. You're already repurposing a dog pen instead of buying a prefab coop that costs as much as a used sedan. Why not embrace the tree? We've seen far too many first-time chicken owners try to sterilize their setup, clear the ground, remove every stick, make it look like a catalog photo, only to have their birds get stressed, bored, or picked off by a hawk because there wasn't a single branch to duck under. Nature is messy. Chickens like messy. They like perching, scratching, and hiding under things. A tree growing through your pen isn't an obstacle. It's a feature.
Now, the practical part. That dog pen might be fine for a labrador, but a raccoon can reach right through chain link and grab a chicken leg. You mentioned bobcats, so you already know the stakes. The plan is: build a fully enclosed coop inside that pen, with hardware cloth over every opening (not chicken wire, that's for keeping chickens in, not predators out). Nesting boxes should be low enough to access but high enough to avoid snakes. And yes, the tree needs respect. Don't nail the coop to the tree. Trees move, sway, grow. Use a free-standing frame that sits around the trunk, with enough gap for expansion. A strap or two to stabilize is fine, but rigid attachment will rip the roof off in three years.
What would we tell a reader who asked? Go for it. But watch the tree's bark. If it starts rubbing against anything, trim or pad. Seal any gaps where a snake could slither in. And name the tree something ridiculous, maybe "Cluck Hollis" or "Branchy McFeatherface", because this setup already has character. You're not starting from scratch. You're starting from a weird, organic, slightly overgrown place, and that's exactly the kind of foundation that turns a coop from a chore into a story. Just make sure the roof is raccoon-proof and the tree doesn't become a ladder for a bobcat. That's the line between cluck-tastic and tragic.