Exchange SE and 365 Hybrid Configuration Wizard (HCW) query

Jon Kilner 136 Reputation points
2026-06-05T12:11:35.19+00:00

We are upgrading our on-prem Exchange environment from 2016 to Exchange SE. The Exchange 2016 environment is hybrid with our 365 tenant. The following points describe our existing setup:

  1. We have over 1000 domains registered on-prem and in 365 which represent different site locations.
  2. All users have a mail address using one of the 1000 domains listed in point 1. These are allocated based on which site they work from. However, every user will also have the same mail address of our default domain which represents the company (@companyname.com).
  3. All our mailboxes are in 365
  4. Inbound email from external recipients goes via on-prem Exchange before being sent to 365
  5. Outbound email goes direct from 365
  6. We aren't using Rich Coexistence, we don't have free/busy sync, the hybrid enterprise app, etc

When we run the HCW on the new SE servers, the only thing we want to do is ensure the SE servers are brought into the organisation and ensure the relevant connectors are created.

When we run the HCW and work through the screens we're presented with the option to select domains. As can be seen in the image below, our primary email domain is selected and Autodiscover is set to False

Screenshot 2026-06-05 125018

The question is:

  1. Can we leave the default selection of our primary domain, which I'm assuming has been imported from the Organisational Configuration stored in AD or do we need to select all 1000 domains.
  2. Do we need to change the Autodisover setting to True on the companyname.com domain?
  3. Do we need to enable Autodiscover for all 1000 other site domains?
  4. What are the consequences of progressing with the settings above or making changes?

Depending on the answer, I may need to ask a follow-up to query the answer.

Thanks in advance

Jon

Exchange | Hybrid management
Exchange | Hybrid management

The administration of a hybrid deployment that connects on-premises Exchange Server with Exchange Online, enabling seamless integration and centralized control.

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Answer accepted by question author
Anonymous
2026-06-05T13:38:49.11+00:00

 

Hi Jon Kilner

Based on my research, I am happy to share additional insights that I have found so far

1/ Can we leave the default selection of our primary domain, which I'm assuming been imported from the Organisational Configuration stored in AD or do we need to select all 1000 domains?

Yes, in your scenario I would leave only the primary/default company domain selected, assuming that is the intended hybrid namespace. You do not need to select all 1000 accepted domains just because they exist as SMTP/accepted domains. 

Microsoft also states that currently 238 domains can be added to one organization relationship, and HCW cannot set up the Exchange Online organization relationship if more than 238 domains are associated with one organization relationship. Therefore, selecting all 1000 domains would not be appropriate and could cause HCW to fail with the documented “maximum allowed number of 250” filter error. 

2/ Do we need to change the Autodisover setting to True on the companyname.com domain? 

No. In this scenario, changing Autodiscover to True does not appear necessary. 

The Autodiscover=True option is mainly useful when multiple domains are included in the hybrid configuration and you want HCW to use one specific domain as the Autodiscover namespace for the selected hybrid domains. Since the recommendation here is to include only companyname.com, there is no practical benefit in forcing companyname.com as the Autodiscover domain. 

3/ Do we need to enable Autodiscover for all 1000 other site domains? 

No. If those 1000 site domains are not required for hybrid coexistence features, they should not be selected in HCW. Enabling or including many domains unnecessarily increases complexity around organization relationship configuration, Autodiscover validation, DNS, and certificate planning.  

4/ What are the consequences of progressing with the settings above or making changes? 

If you proceed with only companyname.com selected and Autodiscover=False, the hybrid domain scope remains limited to companyname.com and avoids adding the 1000 site domains into the hybrid organization relationship. 

Since HCW creates or updates the relevant hybrid connectors, mail flow is expected to work provided the existing routing and certificate configuration are correct. 

If you select all 1000 domains, HCW is likely to fail or become unnecessarily complex because of the documented organization relationship domain limitation. 

Reference: 

I hope this provides additional insight.

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