Add to the search of inactive users multiple OUs

tincho1984 Could you try this?

#Script to disable users that not login for more than 90 days

#Create the report file
$FileName = "DisabledUsers" + (Get-Date).ToString("dd-MM-yyyy") + ".csv"
New-Item -Path "C:\temp" -Name $FileName -ItemType File
Add-Content -Path C:\temp\$fileName -Value "Account,Disabled date,Last Logon Date"
$DisabledDate = Get-Date -Format dd/MM/yyyy
$OUS="OU1","OU2"
foreach ($OU in $OUS) {
$UsersToDisable = Get-ADUser -Filter 'Enabled -eq $True' -SearchBase "$($OU)" -Properties LastLogonDate,WhenCreated | where {$_.LastLogonDate -lt (get-date).AddDays(-90) -and $_.WhenCreated -lt (get-date).AddDays(-90)}

foreach($User in $UsersToDisable){
    if($User.DistinguishedName -notlike "$($OU)"){
        Disable-ADAccount -Identity $User.SamAccountName -Confirm:$false 
        if((Get-ADUser -Identity $User.SamAccountName)){
            $Account = $User.SamAccountName
            $LastLogon = $User.LastLogonDate
            $Value = "$Account,$DisabledDate,$LastLogon"
            Add-Content -Path C:\temp\$FileName -Value $Value
            }
        }
    }
}

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