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My iPhone shows I have two backups of WhatsApp, one in iCloud Storage and the other is included in the iCloud Backup of my iPhone. If I delete the one in iCloud Storage, will it also be deleted from the iCloud Backup?

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Deleting one does not affect the other as they are backups of different types.

  • The backup in iCloud Backup (first screenshot) is a backup of the contents of the app container on your iPhone. This is backed up every night as your iCloud Backup takes place, or manually when you Back Up Now.

  • The ‘backup’ in iCloud Storage (second screenshot) is a backup created by WhatsApp using WhatsApp Settings → Chats → Chat Backup. This is backed up at most per the interval set in WhatsApp settings, or manually when you Back Up Now.

It is up to you which backup you choose to keep. Personally I would use WhatsApp own backup service with iCloud rather than iCloud Backup.

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You might want to keep in mind that when backing up WhatsApp via the second option as explained by grg – the iCloud Storage way – then those backups will trigger all of your Macs with iCloud Drive turned on to sync that WhatsApp data to a hidden file on macOS and affect your storage space on those devices, your bandwidth and in case of laptops your battery life as well (https://apple.stackexchange.com/a/237207/54388).

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