My husband and I are on permit B. He works in Switzerland, so his tax is directly deducted from his salary. I work in a neighboring country and commute, so I need to file taxes myself which I did with the help of an accountant.

The problem is that the amount of joint tax that he calculated is way more than double the tax my husband has paid, although our salaries are more or less the same, and that's taking all the tax discounts we are eligible for, e.g. 3rd pillar, into the account as well. The wealth tax is also negligible in our case. When I asked the accountant about it he said, the tax deducted from my husband salary is not calculated correctly and we both have to pay more. Is this possible?

Taxes for couples are usually more than if they were not married. The marginal tax rate is determined from the combined salary.

How would anyone here be in a better position to assess this than your accountant?

Sounds about right. Your husbands tax rate calculated as if he is the only taxpayer, so he has underpaid. Your accountant has calculated your tax at the correct rate and then added your husband’s underpayment.

You should ask your husband’s employer to calculate his taxes based on your joint salary.