When managing IIS websites through PowerShell, many administrators discover that Stop-Website behaves differently than the IIS Manager GUI. The command only stops the site temporarily - any IIS reset (iisreset.exe) or server reboot will restart the site automatically.

# Temporary stop (won't persist after reset)
Stop-Website "ProductionWebApp"
iisreset
# Site comes back online!

The IIS Manager actually modifies the site's persistent configuration in applicationHost.config (typically located at %windir%\system32\inetsrv\config\applicationHost.config), while Stop-Website only changes the runtime state.

To achieve the same permanent stop behavior as IIS Manager, we need to modify the site's serverAutoStart property:

Import-Module WebAdministration
Set-ItemProperty "IIS:\Sites\ProductionWebApp" -Name serverAutoStart -Value $false
Stop-Website "ProductionWebApp"

For environments without WebAdministration module:

# Disable auto-start
%windir%\system32\inetsrv\appcmd.exe set site "ProductionWebApp" /serverAutoStart:false
# Stop immediately
%windir%\system32\inetsrv\appcmd.exe stop site "ProductionWebApp"

Check your changes in applicationHost.config:

# Should show serverAutoStart="false"
Select-String -Path "$env:windir\system32\inetsrv\config\applicationHost.config" -Pattern "ProductionWebApp"

For multiple sites, use PowerShell pipeline:

Get-ChildItem IIS:\Sites | Where-Object { $_.Name -like "*Test*" } | ForEach-Object {
    Set-ItemProperty $_.PSPath -Name serverAutoStart -Value $false
    Stop-Website $_.Name
}

To reverse the changes:

Set-ItemProperty "IIS:\Sites\ProductionWebApp" -Name serverAutoStart -Value $true
Start-Website "ProductionWebApp"

Many administrators discover that using PowerShell's Stop-Website cmdlet doesn't actually persist the stopped state across IIS resets or server reboots. This behavior differs from manually stopping sites in IIS Manager, which maintains the stopped state persistently.

# Temporary stop (doesn't persist)
Stop-Website 'MyWebsite'
iisreset
# Website comes back online automatically

The key difference lies in how these methods interact with IIS configuration. Stop-Website only changes the runtime state, while IIS Manager modifies the underlying configuration in applicationHost.config.

To make website stops persistent, we need to modify the server configuration directly. Here's the PowerShell approach:

# 1. Import WebAdministration module
Import-Module WebAdministration

# 2. Get the website object
$site = Get-Item "IIS:\Sites\MyWebsite"

# 3. Set the serverAutoStart property to false
$site.serverAutoStart = $false

# 4. Commit the changes
$site | Set-Item

For those who prefer command-line tools, you can achieve the same result with:

appcmd set site "MyWebsite" /serverAutoStart:false

After making these changes, you can verify the setting in applicationHost.config:

# Location: %windir%\system32\inetsrv\config\applicationHost.config
# Look for:
<site name="MyWebsite" serverAutoStart="false">

When you want the site to auto-start again:

# PowerShell method
$site = Get-Item "IIS:\Sites\MyWebsite"
$site.serverAutoStart = $true
$site | Set-Item

# Or using AppCmd
appcmd set site "MyWebsite" /serverAutoStart:true

• This method requires administrative privileges
• Changes affect the site's behavior after any service restart
• Works for both websites and application pools (using similar properties)
• Doesn't immediately stop running instances - combine with Stop-Website if needed