Every business whose turnover exceeds a certain level is obliged to charge VAT on every invoice they issue (unless they’re exempt because they’re an association or a charity or something), that’s the law. The maximum threshold for auto entrepreneur is specifically set at exactly the minimum VAT threshold, and that is why auto entrepreneurs are exempted from charging, because by definition they are below the VAT threshold. Once you exceed the AE threshold, that means that you’re earning too much to qualify for the VAT exemption any longer.
You don’t pay it, you charge it, or to put it a different way, you collect it on behalf of the taxman. The agency charges the client, and you charge the agency. Then you all hand over the VAT you’ve collected to the VAT man, and claim back the VAT you’ve paid. It’s a set rate, I think it’s 20%. It has to appear on a separate line on the invoice.
I’m no expert on VAT but I think it goes something like this:
Job is worth 100€. Agency adds their commission and charges 150€ plus 20% TVA. Client pays 180€. Agency keeps 150 and hands 30€ to the VAT man. If client is VAT registered they subsequently reclaim that 30€ so they have paid 150.
As an AE you invoice the agency 100€, they pay you 100, there is no VAT involved.
As a VAT registered business you invoice 100 + 20%, the agency pays you 120. You keep your 100€ and hand over the extra 20€ to the taxman so you have earned 100. Agency subsequently reclaims 20 so they have paid 100.
The only time the taxman gets to keep the VAT is when somewhere down the line a non-VAT registered purchaser is involved, because they pay it and can’t claim it back. As long as it’s all business to business transactions, it’s just paper pushing and it all balances out, you neither gain nor lose. But in fact you will probably gain by being TVA registered because you’ll be able to reclaim TVA on all your business purchases - computers, software etc - which at present, you can’t.
I may have this entirely arse over tit (because when I see 32000€ starting to loom, I stop work for the year - no way am I ever going to go there) and if that’s the case, I’m sure Fabien or some other helpful person will come along and explain it properly.