WordPress installation on Root Folder & Sub Folder on IIS Server, url conflict

This may help, especially the section on Permalinks in a sub directory installation:

https://www.iis.net/learn/application-frameworks/install-and-configure-php-applications-on-iis/install-wordpress-on-iis

WordPress in both root and subfolder (Windows Server IIS) with pretty permalink (/%postname%/) in both[Solved !!!]

Web.config in Main Root Folder as you want.
//Code—–

<?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <system.webServer>
    <rewrite>
      <rules>
	  		<clear />
			<rule name="MainWordpressFolder" patternSyntax="Wildcard">
				<match url="*"/>
					<conditions>
						<add input="{REQUEST_FILENAME}" matchType="IsFile" negate="true"/>
						<add input="{REQUEST_FILENAME}" matchType="IsDirectory" negate="true"/>
					</conditions>
				<action type="Rewrite" url="index.php"/>
			</rule>
		</rules>
    </rewrite>
  </system.webServer>
</configuration>

//Important point to follow in above code
#Add <clear /> after <rules> started…
#<rule name=”MainWordpressFolder” will be unique in all web.config(s) of your hosting.

Web.config in Sub Folder as you want.

//Code—–

<?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <system.webServer>
    <rewrite>
      <rules>
	  		<clear />
			<rule name="SubWordpressFolder" stopProcessing="true">
				<match url=".*" />
					<conditions>
						<add input="{HTTP_HOST}" pattern="^(www.)?youranotherdomain.com" />
						<add input="{PATH_INFO}" pattern="^/" negate="true" />
					</conditions>
				<action type="Rewrite" url="\your\sub\domain\directory\path\{R:0}" />
			</rule>

			<rule name="SubWordpressFolder-wp" patternSyntax="Wildcard">
				<match url="*"/>
					<conditions>
						<add input="{REQUEST_FILENAME}" matchType="IsFile" negate="true"/>
						<add input="{REQUEST_FILENAME}" matchType="IsDirectory" negate="true"/>
					</conditions>
				<action type="Rewrite" url="index.php"/>
			</rule></rules>
    </rewrite>
  </system.webServer>
</configuration>

//Important point to follow in above code
#Add <clear /> after <rules> started…
#First <rule> needed to be defined carefully as described above.
#Second <rule> will be generated from wordpress admin (on permalink change from settings) after generation of above rule, rename the rule name to any-unique-name-of-your-choice

Enjoy ??

Thanks for the advise! I was truly lost with this crazy IIS stuff.
But….. it did not work until I changed <match url=”*”/> to <match url=”.*”/> in both wp rules

@samrat Saha
Thank you so much, your solution works on my situation.