diff --git a/core/system.go b/core/system.go
index 03c7b6c5..c7f0e5ea 100644
--- a/core/system.go
+++ b/core/system.go
@@ -342,7 +342,6 @@ func runScopeScript(ctx context.Context, options *QodanaOptions, startHash strin
 			options.ConfDirPath(),
 		)
 		log.Infof("Analysing %s", hash)
-		writeProperties(options)
 
 		configAtHash, e := platform.GetQodanaYaml(options.ProjectDir)
 		if e != nil {
@@ -352,6 +351,7 @@ func runScopeScript(ctx context.Context, options *QodanaOptions, startHash strin
 		platform.Bootstrap(configAtHash.Bootstrap, options.ProjectDir)
 		installPlugins(options, configAtHash.Plugins)
 
+		writeProperties(options)
 		exitCode := runQodana(ctx, options)
 		if !(exitCode == 0 || exitCode == 255) {
 			log.Errorf("Qodana analysis on %s exited with code %d. Aborting", hash, exitCode)