When attempting to install System Center Virtual Machine Manger 2012/R2, you might get installation failure due to Webdeploy.msi failed with Windows Installer 1603 error code as below:

 

Looking at the logs, you can see webdeploy is failing to install on the system. The reason it reports is that 3.5 already exist if you take a closer look at the logs. Take a look at the logs snippet below:

As highlighted above, it reports A newer version of Web Deploy was found on this machine. To resolve the installation issue, you must navigate to Programs and Features and uninstall the Web Deploy from there. Once this is uninstalled, you can retry the SCVMM installation and it must pass the web deploy issue now.

The reason why a newer version exists can be related to either SCVMM 2016 has been previously attempted to install on this system, or part of web deploy components have been installed for other application requirements.

 

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