He will not be eligible for Dutch permanent residency if he is living in Germany. Instead, he will be able to remain in Germany by virtue of Directive 2004/38/EC "on the right of citizens of the Union and their family members to move and reside freely within the territory of the Member States."
This gives him a right to move with you to any EU state other than the Netherlands, subject to very circumscribed limitations. It may also allow him to move with you back to the Netherlands under certain circumstances, or in his own right after becoming a permanent resident in Germany (or, of course, a German citizen). If you anticipate moving back to the Netherlands, the details will depend on when you plan to move.
If you hope to move back to the Netherlands within three months after moving to Germany, you will have to do that under Dutch law using a regular family member visa. After three months, however, you can also make use of the free movement rights of EU law to move together to the Netherlands. After five years of "continuous residence" in the Netherlands, he will become a permanent resident of the Netherlands, under Article 16 of the directive. There are some exceptions outlined in Article 17 that can lead to earlier acquisition of permanent residence.