I started playing with a pick made of stone, it gives a great tone but on the downside i find myself hitting my pickups every once in a while. So can i damage the pickups when i hit them with my pick? Its not like crazy hitting kinda thing, but i do hit them.
You'll be fine.
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Been using stone picks for a while.

I don't often hit my pickups, but when I do, I don't see any real damage.* I suspect that, even over the long term, any damage will be so superficial as to be meaningless and inaudible.

* so now you know I am not The Most Interesting Man In The World...
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You won't damage the pickups, but I wouldn't be surprised if you start finding your strings wearing through a little faster.
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The only way you're going to hurt an open pickup, is to damage the tape and break the wound wire. Most of them sit low enough, that it's unlikely you'll do that. You may scratch the plastic, or worse, your guitar's finish, though.

With covered pickups, like on a Gibson LP or PRS, you'll just do cosmetic damage to the gold or silver cover plate and/or finish damage to the guitar's body.

Agreed... You'll probably be changing strings a bit more often.
If it hit anything with enough force with a hard object, of course it's going to damage it. However, an infrequent tap with only the amount of force one should be picking with isn't going to do anything. Long term I could possibly see some superficial damage, but then that would beg the question why on earth you didn't adjust your technique as to not hit the pickup.
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You won't damage the pickups, but I wouldn't be surprised if you start finding your strings wearing through a little faster.


i have an old-ish epiphone SG custom with 3 pickups where the middle pickup has quite a big dent in the cover - no idea how it got there, because it looks like someone's been hitting it with a toffee hammer rather than scraping it with a pick, but the pickup works fine
Rig Winter 2017:

Fender Jazzmaster/Yamaha SG1000
Boss TU-3, DS-2, CS-3, EHX small stone, Danelectro delay
Laney VC30-112 with G12H30 speaker, or Session Rockette 30 for smaller gigs
Elixir Nanoweb 11-49 strings, Dunlop Jazz III XL picks
Shure SM57 mic in front of the amp
yeah i know the strings dont really like my new pick, but the sound is awesome. So i dont mind to buy new strings a little more often.

To be honest i never really quite liked the sound of a pick so i did everything fingerstyle. Thats why i probably hit the pickups in the first place.. because of a lacking technique. Got to work on that.