Signing Installers You Create with Inno Setup
Name the Tool
Assign the Command Line Parameters
Paste in the text you use to sign your executables from the command line. Replace the name of the file to sign with $f. Inno Setup will replace the $f variable with the file that is being signed.
"C:\Program Files\Microsoft Platform SDK for Windows Server 2003 R2\Bin\signtool.exe" sign /f "C:\MY_CODE_SIGNING.PFX" /t http://timestamp.comodoca.com/authenticode /p MY_PASSWORD $f
Update Your [Setup] Section
Now when you build your installers they will be signed.