diff --git a/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java b/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java
index ef232a3bd3..6fd98a6c0a 100644
--- a/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java
+++ b/jOOQ-codegen/src/main/java/org/jooq/util/AbstractGenerator.java
@@ -607,18 +607,29 @@ abstract class AbstractGenerator implements Generator {
      */
     protected void empty(File file, String suffix, Set<File> keep) {
         if (file != null) {
+
+            // Just a Murphy's Law safeguard in case a user misconfigures their config...
+            if (file.getParentFile() == null) {
+                log.warn("WARNING: Root directory configured for code generation. Not deleting anything from previous generations!");
+                return;
+            }
+
             if (file.isDirectory()) {
                 File[] children = file.listFiles();
 
-                if (children != null) {
-                    for (File child : children) {
+                if (children != null)
+                    for (File child : children)
                         empty(child, suffix, keep);
-                    }
-                }
-            } else {
-                if (file.getName().endsWith(suffix) && !keep.contains(file)) {
+
+                File[] childrenAfterDeletion = file.listFiles();
+
+                // [#5556] Delete directory if empty after content was removed.
+                //         Useful if a catalog / schema was dropped, or removed from code generation, or renamed
+                if (childrenAfterDeletion != null && childrenAfterDeletion.length == 0)
                     file.delete();
-                }
+            }
+            else if (file.getName().endsWith(suffix) && !keep.contains(file)) {
+                file.delete();
             }
         }
     }
diff --git a/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java b/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java
index 27384ced17..70cd39f51d 100644
--- a/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java
+++ b/jOOQ-codegen/src/main/java/org/jooq/util/JavaGenerator.java
@@ -257,7 +257,10 @@ public class JavaGenerator extends AbstractGenerator {
         // XXX Generating catalogs
         // ----------------------------------------------------------------------
         log.info("Generating catalogs", "Total: " + database.getCatalogs().size());
+        CatalogDefinition last = null;
         for (CatalogDefinition catalog : database.getCatalogs()) {
+            last = catalog;
+
             try {
                 if (generateCatalogIfEmpty(catalog))
                     generate(catalog);
@@ -268,6 +271,13 @@ public class JavaGenerator extends AbstractGenerator {
                 throw new GeneratorException("Error generating code for catalog " + catalog, e);
             }
         }
+
+        // [#5556] Clean up common parent directory
+        if (last != null) {
+            log.info("Removing excess files");
+            empty(getStrategy().getFile(last).getParentFile(), (scala ? ".scala" : ".java"), files);
+            files.clear();
+        }
     }
 
     private boolean generateCatalogIfEmpty(CatalogDefinition catalog) {
@@ -449,10 +459,6 @@ public class JavaGenerator extends AbstractGenerator {
 
 
 
-        log.info("Removing excess files");
-        empty(getStrategy().getFile(schema).getParentFile(), (scala ? ".scala" : ".java"), files);
-        files.clear();
-
         // XXX [#651] Refactoring-cursor
         watch.splitInfo("Generation finished: " + schema.getQualifiedName());
         log.info("");