It depends on how you set the property. If you are trying to set the property or arguments as an argument to your Eclipse instance then I would expect this to have *no* effect on the Gradle daemon process. The daemon is a separate process.
In recent versions of the tools you should be able to set system properties via the Gradle preferences page accessible via menu
"Window >> Preferences >> Gradle >> Arguments".
Try adding -Dprop=value arguments to either the JVM or program arguments section.
Note: there are also similar sections in the Gradle launch configuration editor (accessible via menu "Run >> External Tools >> External Tools Configuration") Settings specified there for individual launc configuration to run Gradle tasks will override the global defaults specified in the preferences page.
If you are using the preferences page this *should* work. If it does not work then this is a bug and a bug report should be raised.
Presently, I don't think there is a way to set environment variables yet. If you need this ability you should raise a feature request on our issue tracker https://issuetracker.springsource.com/browse/STS
Kris De Volder -- SpringSource