diff --git a/cmd/crowdsec-cli/main.go b/cmd/crowdsec-cli/main.go
index b1092565e..e0955617a 100644
--- a/cmd/crowdsec-cli/main.go
+++ b/cmd/crowdsec-cli/main.go
@@ -66,10 +66,6 @@ func initConfig() {
 		csConfig = csconfig.NewDefaultConfig()
 	}
 
-	if err := csconfig.LoadFeatureFlagsFile(csConfig, log.StandardLogger()); err != nil {
-		log.Fatal(err)
-	}
-
 	// recap of the enabled feature flags, because logging
 	// was not enabled when we set them from envvars
 	if fflist := csconfig.ListFeatureFlags(); fflist != "" {
diff --git a/cmd/crowdsec/main.go b/cmd/crowdsec/main.go
index 05d206168..a6e7c66ad 100644
--- a/cmd/crowdsec/main.go
+++ b/cmd/crowdsec/main.go
@@ -260,10 +260,6 @@ func LoadConfig(cConfig *csconfig.Config) error {
 		return err
 	}
 
-	if err := csconfig.LoadFeatureFlagsFile(cConfig, log.StandardLogger()); err != nil {
-		return err
-	}
-
 	// recap of the enabled feature flags, because logging
 	// was not enabled when we set them from envvars
 	if fflist := csconfig.ListFeatureFlags(); fflist != "" {
diff --git a/pkg/csconfig/crowdsec_service.go b/pkg/csconfig/crowdsec_service.go
index ee6f9d38b..abbe8d255 100644
--- a/pkg/csconfig/crowdsec_service.go
+++ b/pkg/csconfig/crowdsec_service.go
@@ -45,6 +45,10 @@ func (c *Config) LoadCrowdsec() error {
 		return err
 	}
 
+	if err = LoadFeatureFlagsFile(c, log.StandardLogger()); err != nil {
+		return err
+	}
+
 	if c.Crowdsec == nil {
 		log.Warning("crowdsec agent is disabled")
 		c.DisableAgent = true
diff --git a/pkg/csconfig/cscli.go b/pkg/csconfig/cscli.go
index 6b0bf5ae4..f0dac2b76 100644
--- a/pkg/csconfig/cscli.go
+++ b/pkg/csconfig/cscli.go
@@ -1,5 +1,9 @@
 package csconfig
 
+import (
+	log "github.com/sirupsen/logrus"
+)
+
 /*cscli specific config, such as hub directory*/
 type CscliCfg struct {
 	Output             string            `yaml:"output,omitempty"`
@@ -22,6 +26,9 @@ func (c *Config) LoadCSCLI() error {
 	if err := c.LoadConfigurationPaths(); err != nil {
 		return err
 	}
+	if err := LoadFeatureFlagsFile(c, log.StandardLogger()); err != nil {
+		return err
+	}
 	c.Cscli.ConfigDir = c.ConfigPaths.ConfigDir
 	c.Cscli.DataDir = c.ConfigPaths.DataDir
 	c.Cscli.HubDir = c.ConfigPaths.HubDir