My husband is in a similar position. He previously worked for a multinational company based out of Ireland. I got a job in Spain and he came with me and now works for the Spanish office but remains on an Irish contract and is effectively on loan to the Spanish office for a year at a time.
There was various jigs and reels clarifiying his tax status but eventually it turned out that he is liable for PRSI in Ireland (paid directly via his company) and for income tax in Spain. I am resident in Ireland for tax purpuses and so pay every there. We also submit a joint tax return in Ireland for income derived from renting our house out in Ireland and from the sale of shares.
It can be complicated and you will need to get advice, preferably from a company that has offices in Irl and Germany. However, in my experience, such advice is not always reliable either - after submitting two tax returns to Revenue and getting prompt replies from them saying that they were happy with our calculations, the company we get tax advice from proceeded in Year 3 to tell us we could not be assessed jointly as we had different tax statuses! We told them that, since they had not mentioned this the previous two years, we found this a little hard to believe and submitted our joint tax return as usual which was accepted by Revenue as usual. They also screwed up a number of calculations in relation to the Spanish tax side of things.
On the Irish side of things, Revenue have been more than helpful with clarifications and very efficient. My sense is that as long as they see you are attempting to be as compliant as possible and being entirely open, they are not interested in complicating life for you and for themselves.