diff --git a/internal/cmd/root/root.go b/internal/cmd/root/root.go
index 7bd95e1b..cc2c9e1b 100644
--- a/internal/cmd/root/root.go
+++ b/internal/cmd/root/root.go
@@ -60,12 +60,19 @@ func init() {
 			viper.SetConfigType(jiraConfig.FileType)
 		}
 
-		viper.AutomaticEnv()
-		viper.SetEnvPrefix("jira")
+		if err := viper.ReadInConfig(); err == nil {
+			if debug {
+				fmt.Printf("Using config file: %s\n", viper.ConfigFileUsed())
+			}
 
-		if err := viper.ReadInConfig(); err == nil && debug {
-			fmt.Printf("Using config file: %s\n", viper.ConfigFileUsed())
+			// Preserve config file token before AutomaticEnv binds JIRA_API_TOKEN.
+			if token := viper.GetString("api_token"); token != "" {
+				viper.Set("api_token", token)
+			}
 		}
+
+		viper.AutomaticEnv()
+		viper.SetEnvPrefix("jira")
 	})
 }