SharePoint Online: PowerShell to Bulk Check In All Documents

Requirement: Bulk Check in All Documents in SharePoint Online using PowerShell

How to bulk check in documents in SharePoint Online?
How to check in multiple documents in SharePoint Online? Well, You can check-in either a single file or multiple files in a document library by selecting them and choosing "Check in" within few clicks.

However, We have a very large document library with lot of documents checked out and want them to check in to make available to end users. Tried creating a view that filters all checked out files, but failed since the list item count is > 5000 (List view threshold issue!)

SharePoint Online: PowerShell to Check in All Documents
Here is the PowerShell to check in multiple files in SharePoint Online document library.

#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"
  
#Set parameter values
$SiteURL="https://crescent.sharepoint.com/"
$LibraryName="Documents"
 
Try{
    #Get Credentials to connect
    $Cred= Get-Credential
    $Credentials = New-Object Microsoft.SharePoint.Client.SharePointOnlineCredentials($Cred.Username, $Cred.Password)
  
    #Setup the context
    $Ctx = New-Object Microsoft.SharePoint.Client.ClientContext($SiteURL)
    $Ctx.Credentials = $Credentials
 
    #Get the Web
    $Web = $Ctx.Web
    $Ctx.Load($Web)
    $Ctx.ExecuteQuery()
 
    #Get the list
    $List = $Web.Lists.GetByTitle($LibraryName)
 
    #Prepare the query
    $Query = New-Object Microsoft.SharePoint.Client.CamlQuery
    $Query.ViewXml = "@
    <View Scope='RecursiveAll'>
        <Query>
            <Where>
                <IsNotNull><FieldRef Name='CheckoutUser' /></IsNotNull>
            </Where>
        </Query>
        <RowLimit Paged='TRUE'>2000</RowLimit>
    </View>"
 
    #Batch Process items: sharepoint online powershell bulk check in 
    Do {
        $ListItems = $List.GetItems($Query)
        $Ctx.Load($ListItems)
        $Ctx.ExecuteQuery()
 
        $Query.ListItemCollectionPosition = $ListItems.ListItemCollectionPosition
 
        #Get All Checked out files
        ForEach($Item in $ListItems)
        {
            #Get the Checked out File data
            $File = $Ctx.Web.GetFileByServerRelativeUrl($Item["FileRef"])
            $Ctx.Load($File)
            $CheckedOutByUser = $File.CheckedOutByUser
            $Ctx.Load($CheckedOutByUser)
            $Ctx.ExecuteQuery()
 
            Write-Host -f Yellow "Found a Checked out File '$($File.Name)' at $($Web.url)$($Item['FileRef']), Checked Out By: $($CheckedOutByUser.LoginName)"

            #Check in the document
            $File.CheckIn("Checked-in By Administrator through PowerShell!", [Microsoft.SharePoint.Client.CheckinType]::MajorCheckIn)      
            $Ctx.ExecuteQuery()
            Write-Host -f Green "File '$($File.Name)' Checked-In Successfully!"
        }
    }
    While($Query.ListItemCollectionPosition -ne $Null)
}
Catch {
        write-host -f Red "Error Check In Files!" $_.Exception.Message
}

SharePoint Online: Check in Multiple Files using PowerShell
Let's scan the entire site collection for checked out files and check in them back using PowerShell.

#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"
 
#PowerShell to Bulk check-in all documents
Function CheckIn-AllDocuments([String]$SiteURL)
{
    Try{
        #Setup the context
        $Ctx = New-Object Microsoft.SharePoint.Client.ClientContext($SiteURL)
        $Ctx.Credentials = $Credentials

        #Get the Web
        $Web = $Ctx.Web
        $Ctx.Load($Web)
        $Ctx.Load($Web.Webs)
        $Ctx.ExecuteQuery()

        #Get All Lists from the web
        $Lists = $Web.Lists
        $Ctx.Load($Lists)
        $Ctx.ExecuteQuery()
 
        #Prepare the CAML query
        $Query = New-Object Microsoft.SharePoint.Client.CamlQuery
        $Query.ViewXml = "@
        <View Scope='RecursiveAll'>
            <Query>
                <Where>
                    <IsNotNull><FieldRef Name='CheckoutUser' /></IsNotNull>
                </Where>
            </Query>
            <RowLimit Paged='TRUE'>2000</RowLimit>
        </View>"

        #Array to hold Checked out files
        $CheckedOutFiles = @()
        Write-host -f Yellow "Processing Web:"$Web.Url
        
        #Iterate through each document library on the web
        ForEach($List in ($Lists | Where-Object {$_.BaseTemplate -eq 101 -and $_.Hidden -eq $False}) )
        {
            Write-host -f Yellow "`t Processing Document Library:"$List.Title

                #Batch Process List items 
                Do {
                    $ListItems = $List.GetItems($Query)
                    $Ctx.Load($ListItems)
                    $Ctx.ExecuteQuery()

                    $Query.ListItemCollectionPosition = $ListItems.ListItemCollectionPosition

                    #Get All Checked out files
                    ForEach($Item in $ListItems)
                    {
                        #Get the Checked out File data
                        $File = $Web.GetFileByServerRelativeUrl($Item["FileRef"])
                        $Ctx.Load($File)
                        $CheckedOutByUser = $File.CheckedOutByUser
                        $Ctx.Load($CheckedOutByUser)
                        $Ctx.ExecuteQuery()

                        Write-Host -f Green "`t`t Found a Checked out File '$($File.Name)' at $($Web.url)$($Item['FileRef']), Checked Out By: $($CheckedOutByUser.LoginName)"

                        #Check in the document
                        $File.CheckIn("Checked-in By Administrator through PowerShell!", [Microsoft.SharePoint.Client.CheckinType]::MajorCheckIn)      
                        $Ctx.ExecuteQuery()
                        Write-Host -f Green "`t`t File '$($File.Name)' Checked-In Successfully!"
                    }
                }While($Query.ListItemCollectionPosition -ne $Null)
        }

        #Iterate through each subsite of the current web and call the function recursively
        ForEach($Subweb in $Web.Webs)
        {
            #Call the function recursively to process all subsites underneath the current web
            CheckIn-AllDocuments -SiteURL $Subweb.URL
        }
    }
    Catch {
        write-host -f Red "Error Check In Files!" $_.Exception.Message
    }
}

#Config Parameters
$SiteURL="https://crescent.sharepoint.com/"
 
#Setup Credentials to connect
$Cred= Get-Credential
$Credentials = New-Object Microsoft.SharePoint.Client.SharePointOnlineCredentials($Cred.Username, $Cred.Password)
 
#Call the function: sharepoint online powershell to check in all documents in a Site Collection
CheckIn-AllDocuments -SiteURL $SiteURL

If you need to check in a file in SharePoint Online use: PowerShell to Check In a Document in SharePoint Online

PnP PowerShell to Check-In All Files in a Document Library
Here is how to use PnP PowerShell to check in all documents in SharePoint Online document library.

#Parameter
$SiteURL= "https://crescent.sharepoint.com/sites/marketing/"
$ListName = "Documents"

#Connect to PnP Online
Connect-PnPOnline -Url $SiteURL -Credentials (Get-Credential)

#Get All List Items from the List - Filter Files
$ListItems = Get-PnPListItem -List $ListName -PageSize 500 | Where {$_["FileLeafRef"] -like "*.*"}

#Loop through each list item
ForEach ($Item in $ListItems)
{
    Write-host -f Yellow "Testing If file is Checked-Out:"$Item.FieldValues["FileRef"]
    #Get the File from List Item
    $File = Get-PnPProperty -ClientObject $Item -Property File

    If($File.Level -eq "Checkout")
    {
        #Check-In and Approve the File
        Set-PnPFileCheckedIn -Url $File.ServerRelativeUrl -CheckinType MajorCheckIn

        Write-host -f Green "`tFile Checked-In:"$File.ServerRelativeUrl
    }
}