Does each help center in Zendesk need its own application when integrating with Algolia?

Yes! You can now setup multiple Zendesk connectors from the same app, targeting different indices.

When setting up multiple connectors, you can use the same Zendesk help center, or different ones, as long as they are help centers.

You must update the index name in the document_head.hbs file, as mentioned in this doc page, so the indexName is the same as the one put in the connector’s destination.