Applying for spouse visas during the pandemic

There is no other way to get a visa than through the embassy.
Could you try to send them the required papers by post?
Or apply in another country, where the embassy works better?

Hi, we are already in Berlin, it doesn't make sense to go to some other embassy now, does it?  And the embassies will only allow visits from people in the country where they are, so at this point this route is impossible

If you are already in Germany, I assume you hold the required spouse visa (the headline is misleading in this case!) and want to apply for the residence permit now.
For that, you need to first register your residential address at the town hall. Then contact your local foreigner authority ("Auländerbehörde") for an appointment. They are usually slow and overworked, but you have to apply there.

No, we got married on January 23 and they have not processed applications since early December. So please let me know how could we have gotten the spouse visa?

Now the situation is different again!
So she is already in Germany, but not on a family reunion visa (FRV or "Visum zum Familiennachzug" in German)?
Does she hold a marriage visa ("Heiratsvisum") instead?
If so, applying for a residence permit at the foreigner authority ("Ausländerbehörde") is the correct next step (and there is, unfortunately, no alternative).
If not, she needs to apply for an FRV first - at the German embassy in her home country!
Only after entering Germany with a FRV can she apply for a residence permit at the foreigner authority.
I hope this clarifies the confusion.

beppi wrote:

There is no other way to get a visa than through the embassy.

There is just one embassy in a country - but in larger ones there can be multiple consulates that usually do such consular services.

An American married to an EU citizen IS allowed to enter Germany without a visa and file their application here. We have checked this on multiple official web sites and we were checked both by border control and police and they had no objections, plus had it confirmed by a lawyer. I would guess that they know more about it than yourself.