Setting up multiple O365 organisation accounts on iOS I was about to setup the mail account my customer provided me. Being a O365 Outlook account, I was approaching this with selecting Exchange as account type and signed in. This would have worked well, but the tennant asks for managing my device by the Intune Company Portal app. However, my device is already managed by the company I'm working for via Intune.

My fear is, when I allow Intune to manage my device, it'll probably kill the configurations made through my company's administrator.

Anybody having experience with such a setting and is willing to share what they know?
Going off the title question - Setting up multiple O365 organisation accounts on iOS and interpreting that to mean you want to have multiple Intune profiles on a single iOS device because you (or your customer) has multiple accounts managed by different Intune servers; unfortunately, the answer is no, this cannot be done.


  Intune only supports deploying app protection policies to only one user account per device.


Microsoft details this in their support document What to expect when your iOS app is managed by app protection policies.


  Read the following example scenario to learn how Intune handles
  multiple user accounts.
  
  User A works for two companies: Company X, and Company Y. User A has a
  work account for each company, and both use Intune to deploy app
  protection policies. Company X deploys app protection policies before
  Company Y. The account associated with Company X will get the app
  protection policy, but not the account associated with Company Y. To
  have the Company Y user account managed by the app protection
  policies, User A must remove the Company X user account.