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If I change the SharePoint service application pool like "user profile sync and search services" to a new one with a new account from service properties.

What's gonna happen to the service?

it this will affect the service or change anything for users or what?

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If you plan it properly, it will not impact any thing. You have to make sure that account under which new app pool run should have proper permission and do in off hours. I am sure When you change the App pool for a service application may be you need to reset IIS and it will cause a brief outage.

You can use the following code example to change the pool.

#List All Applicatino Pools 
Get-SPServiceApplicationPool 

$BDCSetting = Get-SPServiceApplication | ? TypeName -like "Business Data Connect*" | Select ID, TypeName, ApplicationPool 
Get-SPServiceApplicationPool $BDCSetting.ApplicationPool 

#Pick the Managed Account assigned to BDC AppPool 
$MA = Get-SPManagedAccount -Identity $BDCSetting.ApplicationPool.ProcessAccount.Name 
#Create New Application Pool 
$BDCAppPoolName = "BDC Application Pool" 
$BDCAppPool = New-SPServiceApplicationPool -Name $BDCAppPoolName  -Account $MA -Verbose 

#Confirm 
Get-SPServiceApplicationPool -Identity $BDCAppPoolName 

#Change the application Pool and update the service application 
$BDC = Get-SPServiceApplication $BDCSetting.Id 
$BDC.ApplicationPool = $BDCAppPool 
$BDC.Update() 

#Confirm  
$BDC = Get-SPServiceApplication $BDCSetting.Id 
$BDC.ApplicationPool 

https://gallery.technet.microsoft.com/office/Change-SharePoint-Service-d6797f5b

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Doing this though SharePoint Central Admin will not be any impact . , but before that , some something you need pay attention to :

  1. Make sure the new account have enough permission and would be a domain user .
  2. Stop the service and do the changes .
  3. After changes , you need perform IIS reset , it will cause about 1min downtime .

About how to modify APP pool using Central Admin :

https://social.technet.microsoft.com/Forums/en-US/3348b639-9368-49d7-90cb-a174aa08e3ac/how-to-change-the-service-applications-application-pool?forum=sharepointadminprevious

Using PowerShell :

http://dinushaonline.blogspot.sg/2014/01/change-application-pool-of-existing.html

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