Temporary VAT reduction by 3% until 31.12.2020

Ok, if your contract is only with the planning company regarding the design and construction of the house, then my (layman’s) opinion is that the planning company owes you a total invoice taking into account the payments already made and with 16% VAT on the entire amount (since acceptance is only in the second half of the year). I would also have paid only my contractual partner and not the trades, but that is now history. Do you have written confirmation from the planning company that you should pay the trades directly?

I now dare to doubt that a construction manager has the tax knowledge to figure this out. I wouldn’t rely on that statement.

That’s true, but his personal tax advisor seems to know what he’s doing. They probably had to put in a lot of effort last week to correct the old invoices.

When you transfer the invoices, take the entire net amount of the final invoice (if the total sum is shown there), calculate 16% on it and subtract all gross payments made.

I list it to the companies like this:
Gross amount incl. 19% VAT = €119
Net amount = €100
Gross amount incl. 16% VAT = €116
General costs = -€15
Total costs = €101
Already paid = -€90
Open amount = €11

I think nothing can go wrong with this.

I list it to the companies as follows:
Gross amount incl. 19% VAT = €119
Net amount = €100
Gross amount incl. 16% VAT = €116
Generalien = -€15
Total costs = €101
Already paid = -€90
Outstanding amount = €11

I think nothing can go wrong with this.

Basically looks good.
But what are Generalien?

But what are general items?

Costs proportionally allocated to all trades for construction fences, construction debris containers, etc.

The first company has already opposed and does not agree with my invoice. According to their statement, the service has already been rendered and since the final invoice was issued on 05.05, 19% would be due on all invoices. Even though no acceptance had taken place at that time. However, the contract states, "A security retention of 5% of the contract amount including VAT will be withheld by the client until the completion of the respective service and the remedy of defects." And this 5% invoice was the one that was in our mail yesterday after the acceptance from two weeks ago.

It doesn't matter at all when he finished the work, even if you had already paid the 5%, the service would only have been rendered upon acceptance. The only problematic issue would be if the site manager on behalf of the planning company possibly made some kind of preliminary acceptance back then. That's why the construction setup here is highly unusual. The contracting party is the planning company. Basically, they should handle this for you. But in the end, as already discussed above, you need a tax specialist...

As you yourself have noted, the security retention can be withheld until the last defect has been remedied. However, defects have nothing to do with completion or acceptance.

If you had a VOB contract, according to a ruling, the final invoice would probably be considered as an indication that the work is completed. After that, the VOB allows a period of 12 working days for acceptance. If this does not happen and no agreement is made on a date, acceptance is automatically deemed to have occurred after the 12 working days. If the tax office argues this way, then acceptance has already occurred by corresponding behavior in May/June.
No idea if there is anything similar for contracts under the Construction Code. Besides, no one knows your contracts in detail.

Therefore, in such a disputed case, I would also act like this as a craftsman. For the 3%, you are not liable, but the craftsman is, and after 5 years you will not be willing to pay the 3% afterwards if the tax audit at the craftsman then finds something to the contrary.