How do I Save Email using the Email Trigger to MSG format rather than eml format?

Not possible right now. You have to find a converter tool for that.

I am moving this topic to Feature requests.

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Can also change the folder created when the email is saved, it currently creates a number folder.

You can only change the base folder. But the numbering comes from the actual id of the email. We need to store them separately so that attachments do not overwrite each other.

What you can do is to use a file trigger to monitor base (and its sub folders) and then do whatever you want with the file as the email is saved.

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If your system uses an email trigger that only saves messages in .eml format by default, but you prefer .msg (Outlook’s native format), there’s a convenient workaround: use an EML converter tool such as MigrateCloud EML Converter Tool. After your trigger drops the email as .eml, you run the converter to transform it into .msg, preserving metadata, attachments, and formatting. This lets you keep your automation flow intact while storing messages in the format Outlook handles more seamlessly. Let me know if you want a sample automation script to integrate this.