A simple way to run a spring application in Windows Server is to run it as a service. You can do it using the winsw, that you download its .bin file here
winws download
Then, rename it to something like my-app.exe and create a XML file like this:
<service>
<id>my-app-service</id>
<name>my-app-service</name>
<description>Back end service for app</description>
<env name="HOME" value="YOUR_JAR_FILE_PATH"/>
<executable>java</executable>
<arguments>-Xrs -Xmx256m -jar "YOUR_JAR_FILE_PATH\YOUR_JAR_FILE.jar"</arguments>
<logmode>rotate</logmode>
</service>
Then, using the terminal, run:
my-app.exe install service
Your application is now a windows service and you can start\stop it in the tasks manager on the services tab.