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We all know that there are tons of thuja leaves after pruning thuja hedges.

Can thuja leaves be used as mulch (perhaps for acid-loving plants, let's say young pines, or vaccinum)? What if they are put in a compost pile?

I've read something about thujaplicin, thujone, and acetic acids as being present in thuja leaves? Are they harmful or helpful?

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Pretty much any organic material can be used as a mulch or composted, so yes you can do that. I personally toss stuff like that into my long term compost pile that I let break down for a few years before it is usable. Either that or I'll just leave the clippings where they land and cover them up with a better looking mulch. I wouldn't think too hard about specific plant constituents and their affect on compost and/or soil as that involves very complex chemical and biologic processes and I doubt it really makes much of a difference once it breaks down.

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