Full Guide: Windows Server In-Place Upgrade vs Clean Install

Learn the difference between Windows Server in-place upgrade and clean install from this article. Then choose the most suitable upgrade method according to your needs.


By Maggie / Updated on September 28, 2023

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User Case

In-Place OS Upgrade vs Fresh Install

“I'm debating whether to try to perform an in-place OS upgrade from 2012 to 2016 on some of my VM's. Since the underlying hardware really isn't a factor, it seems logical to not have to constantly rebuild servers to upgrade to a new OS. If anyone has had positive or negative results from doing so or any other experiences to share regarding this, I'd appreciate the input. Thanks!”

- Question from Reddit

Clean Install vs Upgrade - What Is the Difference?

If you decide to upgrade to a newer version of Windows Server, you can do it in two ways: in-place upgrade and clean install. Some users are not clear about the difference between them, the following will provide you with a detailed description.

Windows Server In-Place Upgrade VS Clean Install

Upgrade or In-Place Upgrade: move from an older version of the operating system to a newer version, while staying on the same physical hardware. All settings, programs and files will be preserved, you don't need to format the hard drive.

Clean Install: move from an older version of the operating system to a newer version, deleting the older operating system. This will format the hard drive and start a Windows Server clean install.

Windows Server In-Place Upgrade vs Clean Install - Cons and Pros

★ In-Place Upgrade in Windows Server

Pros Cons
It is a commonly used upgrade method for users because it is very simple. With Windows Update Assistant, the process is almost automated, so hardly any technical skills are required. If for any reason you do not want to keep the new version of Windows Server, it also allows you to return to the previous system version. With an in-place upgrade, Windows tries to bring everything from the old version to the new version, which results in the accumulation of many old and unused files, registry entries of certain uninstalled programs, and all other types of garbage. In addition, some programs may not be compatible with the new version.

★ Clean Install in Windows Server

Pros Cons
A fresh installation is a good way to start over, especially if you have been running the same system version for a long time. A clean installation will only install the apps you need and re-control your system apps, starting with a clean Windows Registry. For many users, the worst part of a fresh install may be that all data will be wiped off. You need to back up your personal files and create an installation media with Windows installer. What’s more, you need to have some technical skills as well. After performing a clean install, you need to spend some time re-personalizing your PC.

Stepwise Guide to Perform Windows Server Clean Install and In-Place Upgrade

After comparing Windows Server in-place upgrade vs clean install in detail, I believe you have a choice based on your own situation. So next, I will give you a detailed introduction on how to perform these two operations.

Perform an In-Place Upgrade in Windows Server

As we all know, the latest version of Windows Server is Windows Server 2022. We realize that it is not always possible to perform in-place upgrade to Windows Server 2019. You can use the figure below to determine which version of Windows Server you can upgrade to based on the version you are currently using:

In-Place Upgrade

Then I will show you how to upgrade Windows Server 2012 R2 to 2019 for free step by step.

Preparation before upgrading:

>> Patch your Windows Server 2012 R2 with the latest updates.
>> Insert and mount the Windows Server 2019 setup media.

>> Before upgrading, Microsoft suggests you to collect some information of the device. You can use it for troubleshooting purpose when the upgrade fails.

Note✍: Although the in-place upgrade should theoretically not delete any content, there are also cases of data loss. Therefore, it is strongly recommended that you use the backup software described in the next section to back up the operating system and important data.

  1. Locate the Windows Server 2019 setup media, run setup.exe directly.

Windows Server 2019 Setup Media

  1. Select Download updates, drives and optional features (recommended) and click Next.

Windows Server 2019 Setup

  1. Setup checks your device configuration, you must wait for it to finish, and then select Next.

Tip✍: Depending on the distribution channel that you received Windows Server media from (retail, volume licensing, OEM, ODM, etc.) and the license for the server, you may be prompted to enter the license key to continue.

  1. Select the version of Windows Server 2019 you want to install and click Next.

Select Image

  1. Accept the terms and then select Keep personal files and apps to choose to do an in-place upgrade, and then select Next.

Choose What to Keep

  1. After Setup analyzes your device, it will prompt you to proceed with your upgrade by selecting Install.


  1. Then upgrade Windows Server 2012 R2 to 2019 for free will begin. After the upgrade is complete, your server will restart.


After your upgrade is done, you must make sure the upgrade was successful. You can open Registry Editor and go to HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\WindowsNT\CurrentVersion to check the edition of your Windows Server in ProductName.

Perform a Clean Install in Windows Server

Here, I will show you how to perform a clean installation of Windows Server 2019 as an example.

Preparation before installing:

>> Download the Windows Server 2019 ISO file from Microsoft and burn Windows Server 2019 ISO to USB (over 8 GB) for installation.

  1. Insert the USB installation media, restart your PC and set boot from the USB.
  2. In the Windows Setup page. Enter your language and other preferences and click Next to continue.

Windows Setup

  1. Click Install Now to start out the Windows Server 2019 installation.

Install Now

  1. Select the version of Windows Server 2019 you want to install and click Next.

Windows Server 2019 Standard

  1. Then, accept the license terms and select Custom: Install Windows only (advanced) to perform a fresh install.

Select the Installation Type

  1. Select the destination to install the Windows Server and click on Next.

Select A Partition to Install

  1. The installation will begin, wait for it to complete. The system should restart automatically after installation.

Backup Windows Server to Avoid Any Data Loss

Although in-place upgrade is relatively easy, it is not recommended. If you perform a clean install of Windows Server, you will have a clean computer that performs better than an in-place upgrade. However, both methods can result in a data loss situation, and a clean install will delete all your original data. So, it is recommended that you back up your server in advance before performing either of these operations to prevent any data loss.

AOMEI Backupper Server is a full-featured backup and recovery software for all Windows Servers (Server 2003/2008 (R2)/2012 (R2)/2016/2019/2022) and PCs. It provides continuous data protection for business and makes all data backup and disaster recovery works easy. No professional skills or technologies required.

It supports you to back up Server to different storages. For instance, backup Server to external hard drive, NAS, network share, cloud service, etc. No matter what accidents happen, you can restore your backups from these places.

The following is a graphic tutorial to show you how to back up Windows Server through AOMEI Backupper.

Step 1. Download and install AOMEI Backupper Server to your computer. Besides this version, you can also use AOMEI Backupper Technician Plus to protects priceless data and system on unlimited PCs and Servers.

Download Free Trial Windows Server & PC
Secure Download

Step 2. Launch this software. In the dark blue interface, click Backup in the left panel and then select System Backup Windows Server backup.

System Backup

Step 3. The program will automatically select the system partitions by default. Click the box below the arrow to select the destination to save the Windows Server image backup.

Select Path

Step 4. Click Start backup to back up Windows Server.

Start Backup

Tips on long-term data protection✍:
✮ Options: You can configure task specific settings, including the compression level, backup encryption, notifications, splitting image, intelligent sector, VSS, and more.
Schedule Backup: You can specify the exact time you want the backup to run, which is useful if you want to protect your data for a long time.
You can set a specific time of day, any day of the week or month, or event triggers, USB plug in.
✮ Backup Scheme: It offers 3 common backup schemes, including full backup, incremental backup and differential backup. It will automatically delete backup image files according to the type of scheme you choose, which is quite helpful for saving disk space and keeping all backups up to date.


Windows Server in-place upgrade vs clean install, you may have a complete understanding of both after reading this article. But whichever upgrade method you choose, it is recommended that you make a backup of your server in advance. Besides AOMEI Backupper Server, you can also use another tool - AOMEI OneKey Recovery to backup your system, which can help you boot your computer directly and successfully without the need of a boot disk.

Maggie · Editor
Maggie is a technical editor from AOMEI and troubleshoots technical problems against data protection. She has received professional and systematic technical training. With a focus on user experience, security, and problem-solving, she always puts herself in the readers' shoes and provides them with valuable technical insights.