I'm Protestant, he's Catholic, can we have two ceremonies?

Have you thought about or asked either church about having a combined ceremony? I don't think there is any reason you couldn't have two church ceremonies if that's important to you, though there may be a way to combine them. I don't think the order matters either. People get married in civil ceremonies and then have a religious ceremony later all the time, and this situation seems similar to that.

You may want to start with inquiring with the Catholic church, as there are a lot of rules for a Catholic wedding.

We had a catholic wedding. I am catholic my husband is not nor does he attend church.
During our planning process the priest asked if there was another minister that we wanted to participate in the ceremony. Maybe you can do this?
I also believe his priest can give permission to have the ceremony in your nondenominational church. Your best bet is to have a talk with his priest. He will be able to give you the best answers as each parish can have slightly different allowances. They even asked us if we wanted to write our own vows, which I though was a huge no-no in catholic weddings.

I am Methodist and married a Catholic. We got married in the Catholic church, but, only had a wedding ceremony and not a Catholic mass with communion, hymns, alter boys, etc. It worked out perfectly for us. Tell the Priest you prefer just a ceremony and it will be fine without needing 2 separate ceremonies.

Following in a similar situation!

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This, or a ceremony with officiants of both denominations, would be your best bet!

Countless people have a single ceremony where one is Catholic and the other Protestant and still honor both faiths. Decide which church you will have the ceremony in and talk to the minister/priest on how to put together a ceremony that works for you. It's really alot more commonplace than you think.

Plus, guests will appreciate one ceremony instead of trying to schedule for 2, that they may not be able to get time off for or afford to attend.