SharePoint Online: Delete All Files and Sub-Folders from a Folder Recursively using PowerShell

Requirement: Empty a Folder in SharePoint Online document library by deleting all its files and Sub-Folders recursively.

PowerShell to Delete All Files and Sub-Folders from a SharePoint Online Folder
Let's delete a folder with subfolder and files from SharePoint Online.

#Load SharePoint CSOM Assemblies
Add-Type -Path "C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\16\ISAPI\Microsoft.SharePoint.Client.dll"
Add-Type -Path "C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\16\ISAPI\Microsoft.SharePoint.Client.Runtime.dll"

#Function to Delete all files and Sub-folders of a given Folder
Function Empty-SPOFolder([Microsoft.SharePoint.Client.Folder]$Folder)
{
    Try {
        #Get All Files from the Folder
        $Ctx = $Folder.Context
        $Files = $Folder.Files
        $Ctx.Load($Files)
        $Ctx.ExecuteQuery()
 
        #Iterate through each File in the Root folder
        Foreach($File in $Files)
        {
            #Delete the file
            $Folder.Files.GetByUrl($File.ServerRelativeUrl).Recycle() | Out-Null
            Write-host -f Green "Deleted File '$($File.Name)' from '$($File.ServerRelativeURL)'"
        }
        $Ctx.ExecuteQuery()
 
        #Process all Sub Folders of the given folder
        $SubFolders = $Folder.Folders
        $Ctx.Load($SubFolders)
        $Ctx.ExecuteQuery()
        Foreach($Folder in $SubFolders)
        {
            #Exclude "Forms" and Hidden folders
            If( ($Folder.Name -ne "Forms") -and (-Not($Folder.Name.StartsWith("_"))))
            {
                #Call the function recursively to empty the folder
                Empty-SPOFolder -Folder $Folder

                #Delete the folder
                $Ctx.Web.GetFolderById($Folder.UniqueId).Recycle() | Out-Null
                $Ctx.ExecuteQuery()
                Write-host  -f Green "Deleted Folder:"$Folder.ServerRelativeUrl
            }
        }
    }
    Catch {
    write-host -f Red "Error:" $_.Exception.Message
    }
}

#Variables
$SiteURL = "https://crescent.sharepoint.com/Sites/Marketing"
$ServerRelativeUrl= "/Sites/Marketing/Project Documents/2018"

Try {
    #Get Credentials to connect
    $Cred= Get-Credential

    #Setup the context
    $Ctx = New-Object Microsoft.SharePoint.Client.ClientContext($SiteURL)
    $Ctx.Credentials = New-Object Microsoft.SharePoint.Client.SharePointOnlineCredentials($Cred.Username, $Cred.Password)
  
    #Get the web from URL
    $Web = $Ctx.web
    $Ctx.Load($Web)
    $Ctx.executeQuery()

    #Get the Folder object by Server Relative URL
    $Folder = $Web.GetFolderByServerRelativeUrl($ServerRelativeUrl)
    $Ctx.Load($Folder)
    $Ctx.ExecuteQuery() 

    #Call the function to empty Folder
    Empty-SPOFolder $Folder

    #Delete the given Folder itself
    Write-host  -f Green "Deleting Folder:"$Folder.ServerRelativeUrl
    $Folder.Recycle() | Out-Null
    $Ctx.ExecuteQuery() 
}
Catch {
    write-host -f Red "Error:" $_.Exception.Message
} 

This PowerShell script deletes all files, sub-folders of a folder and then deletes the given folder too.

PnP PowerShell to Empty Folder in SharePoint Online: 
Here is the PnP PowerShell script to clear all files and sub-folders of a given folder in SharePoint Online document library.

#Parameters
$SiteURL = "https://crescent.sharepoint.com/sites/Marketing"
$FolderSiteRelativeURL = "/Shared Documents/2018"

#Connect to the Site
Connect-PnPOnline -URL $SiteURL -Credentials (Get-Credential)

#Get the web & folder
$Web = Get-PnPWeb
$Folder = Get-PnPFolder -Url $FolderSiteRelativeURL

#Function to delete all Files and sub-folders from a Folder
Function Empty-PnPFolder([Microsoft.SharePoint.Client.Folder]$Folder)
{
    #Get the site relative path of the Folder
    If($Web.ServerRelativeURL -eq "/")
    {
        $FolderSiteRelativeURL = $Folder.ServerRelativeUrl
    }
    Else
    {        
        $FolderSiteRelativeURL = $Folder.ServerRelativeUrl.Replace($Web.ServerRelativeURL,"")
    }

    #Delete all files in the Folder
    $Files = Get-PnPFolderItem -FolderSiteRelativeUrl $FolderSiteRelativeURL -ItemType File
    ForEach ($File in $Files)
    {
        #Delete File
        Remove-PnPFile -ServerRelativeUrl $File.ServerRelativeURL -Force -Recycle
        Write-Host -f Green ("Deleted File: '{0}' at '{1}'" -f $File.Name, $File.ServerRelativeURL)        
    }

    #Process all Sub-Folders
    $SubFolders = Get-PnPFolderItem -FolderSiteRelativeUrl $FolderSiteRelativeURL -ItemType Folder
    Foreach($SubFolder in $SubFolders)
    {
        #Exclude "Forms" and Hidden folders
        If(($SubFolder.Name -ne "Forms") -and (-Not($SubFolder.Name.StartsWith("_"))))
        {
            #Call the function recursively
            Empty-PnPFolder -Folder $SubFolder

            #Delete the folder
            Remove-PnPFolder -Name $SubFolder.Name -Folder $FolderSiteRelativeURL -Force -Recycle
            Write-Host -f Green ("Deleted Folder: '{0}' at '{1}'" -f $SubFolder.Name, $SubFolder.ServerRelativeURL)
        }
    }
}

#Call the function to empty folder
Empty-PnPFolder -Folder $Folder

To delete a folder in SharePoint Online document library, use: SharePoint Online: How to Delete a Folder using PowerShell?

The above script deletes folder with files in SharePoint Online! How about deleting a large folder with its files and sub-folders in batches to avoid any potential list view threshold exceeded issue?

#Config Variables
$SiteURL = "https://crescent.sharepoint.com/sites/marketing"
$ListName ="Branding"
$FolderServerRelativeURL = "/sites/Marketing/Branding/2019"

Try {
    #Connect to PnP Online
    Connect-PnPOnline -Url $SiteURL -UseWebLogin
     
    #Get All Items from Folder in Batch
    $ListItems = Get-PnPListItem -List $ListName -FolderServerRelativeUrl $FolderServerRelativeURL -PageSize 2000 | Sort-Object ID -Descending
 
    #Powershell to delete all files from folder
    ForEach ($Item in $ListItems)
    {
        Remove-PnPListItem -List $ListName -Identity $Item.Id -Recycle -Force
        Write-host "Removed File:"$Item.FieldValues.FileRef
    }
}
Catch {
    write-host "Error: $($_.Exception.Message)" -foregroundcolor Red
}

To delete multiple folders in SharePoint Online from a CSV file, use: Bulk Delete Folders from in SharePoint Online from a CSV using PowerShell?