diff --git a/jOOQ-codegen/src/main/java/org/jooq/codegen/GenerationTool.java b/jOOQ-codegen/src/main/java/org/jooq/codegen/GenerationTool.java
index caad18ef67..34bb217c73 100644
--- a/jOOQ-codegen/src/main/java/org/jooq/codegen/GenerationTool.java
+++ b/jOOQ-codegen/src/main/java/org/jooq/codegen/GenerationTool.java
@@ -189,8 +189,11 @@ public class GenerationTool {
                     return;
                 }
 
+                // [#10463] Make sure logging threshold is set, in this special case
+                Configuration configuration = load(in);
+                setGlobalLoggingThreshold(configuration);
                 log.info("Initialising properties", file);
-                generate(load(in));
+                generate(configuration);
             }
             catch (Exception e) {
                 log.error("Cannot read " + file + ". Error : " + e.getMessage(), e);
@@ -244,32 +247,8 @@ public class GenerationTool {
 
     @SuppressWarnings("unchecked")
     private void run0(Configuration configuration) throws Exception {
-        if (Boolean.getBoolean("jooq.codegen.skip")) {
-            log.info("Skipping jOOQ code generation");
-            return;
-        }
-
         if (configuration.getLogging() != null) {
-            switch (configuration.getLogging()) {
-                case TRACE:
-                    JooqLogger.globalThreshold(Level.TRACE);
-                    break;
-                case DEBUG:
-                    JooqLogger.globalThreshold(Level.DEBUG);
-                    break;
-                case INFO:
-                    JooqLogger.globalThreshold(Level.INFO);
-                    break;
-                case WARN:
-                    JooqLogger.globalThreshold(Level.WARN);
-                    break;
-                case ERROR:
-                    JooqLogger.globalThreshold(Level.ERROR);
-                    break;
-                case FATAL:
-                    JooqLogger.globalThreshold(Level.FATAL);
-                    break;
-            }
+            setGlobalLoggingThreshold(configuration);
         }
         else {
             String property = System.getProperty("jooq.codegen.logging");
@@ -284,6 +263,11 @@ public class GenerationTool {
             }
         }
 
+        if (Boolean.getBoolean("jooq.codegen.skip")) {
+            log.info("Skipping jOOQ code generation");
+            return;
+        }
+
         if (log.isDebugEnabled())
             log.debug("Input configuration", "" + configuration);
 
@@ -909,6 +893,31 @@ public class GenerationTool {
         }
     }
 
+    private static void setGlobalLoggingThreshold(Configuration configuration) {
+        if (configuration.getLogging() != null) {
+            switch (configuration.getLogging()) {
+                case TRACE:
+                    JooqLogger.globalThreshold(Level.TRACE);
+                    break;
+                case DEBUG:
+                    JooqLogger.globalThreshold(Level.DEBUG);
+                    break;
+                case INFO:
+                    JooqLogger.globalThreshold(Level.INFO);
+                    break;
+                case WARN:
+                    JooqLogger.globalThreshold(Level.WARN);
+                    break;
+                case ERROR:
+                    JooqLogger.globalThreshold(Level.ERROR);
+                    break;
+                case FATAL:
+                    JooqLogger.globalThreshold(Level.FATAL);
+                    break;
+            }
+        }
+    }
+
     private Properties properties(List<Property> properties) {
         Properties result = new Properties();