My bank account and investment accounts are prefilled in the tax return form and they are above the tax free limit.
Should I overwrite these to 0 or leave them filled? Or there is another way to do this with 30% ruling?
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I am not a tax advisor. However, I used to benefit from the 30% ruling and I've been into the same situation.
Pre-filling of the tax declaration by the Belastingdienst (tax authority) is a common practice. I think it's done by an automated system and it does not know whether you are exempt from anything.
It also happened to me a couple of years ago. I had some savings that exceeded the tax-free limit and it was pre-filled in my tax declaration. I simply removed them from the declaration and went forward with the submission.
The rationale behind this was the fact that if you come to live in the Netherlands and you are eligible for the 30% facility, you can opt for the partial non-resident tax status. With partial non-resident taxpayer status, you are considered a non-resident taxpayer for part of the income tax. As a consequence, you may become exempt from the Box 3 taxation which corresponds to the taxation of savings. The official website of the Belastingdienst explains it all here.
Again, I'm not an advisor. I'm only a fellow expat. So, please read the official website of the tax authority and consult them if you are in doubt. They have a helpline from which you can ask for concrete advice in English. You can contact them on 0800 0543.