An end-to-end secure cloud-hosted collaboration service is provided with a hybrid cloud/on-premise index and search capability. This approach includes on-premise indexing and search handling, while relying on the cloud for persistent storage and search of the index. The on-premise indexer receives a copy of an encrypted message from the cloud-hosted collaboration service. The encrypted message has been encrypted with a conversation key. The indexer receives the conversation key from an on-premise key management service, and decrypts the encrypted message with the conversation key. A set of tokens are extracted from the decrypted message, and subsequently encrypted with a secret key, different than the conversation key, to generate a first set of encrypted tokens. The first set of encrypted tokens is transmitted for storage in a search index on the cloud-hosted collaboration service.