diff --git a/common/dialogs/panel_embedded_files.cpp b/common/dialogs/panel_embedded_files.cpp
index 96861efad2..14dd5039fc 100644
--- a/common/dialogs/panel_embedded_files.cpp
+++ b/common/dialogs/panel_embedded_files.cpp
@@ -21,6 +21,8 @@
  * 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 
+#include <eda_item.h>
+#include <confirm.h>
 #include <bitmaps.h>
 #include <dialogs/panel_embedded_files.h>
 #include <embedded_files.h>
@@ -192,6 +194,51 @@ bool PANEL_EMBEDDED_FILES::TransferDataToWindow()
 
 bool PANEL_EMBEDDED_FILES::TransferDataFromWindow()
 {
+    std::optional<bool> deleteReferences;
+
+    auto confirmDelete =
+            [&]() -> bool
+            {
+                if( EDA_ITEM* parent = dynamic_cast<EDA_ITEM*>( m_files ) )
+                {
+                    if( parent->Type() == PCB_T )
+                    {
+                        return IsOK( m_parent, _( "Deleted embedded files are also referenced in some footprints.\n"
+                                                  "Delete from footprints as well?" ) );
+                    }
+                    else if( parent->Type() == SCHEMATIC_T )
+                    {
+                        return IsOK( m_parent, _( "Deleted embedded files are also referenced in some symbols.\n"
+                                                  "Delete from symbols as well?" ) );
+                    }
+                }
+
+                wxFAIL_MSG( wxT( "Unexpected embedded files owner" ) );
+                return false;
+            };
+
+    for( const auto& [name, file] : m_files->EmbeddedFileMap() )
+    {
+        if( !m_localFiles->HasFile( name ) )
+        {
+            m_files->RunOnNestedEmbeddedFiles(
+                    [&]( EMBEDDED_FILES* nested_files )
+                    {
+                        if( nested_files->HasFile( name ) )
+                        {
+                            if( !deleteReferences.has_value() )
+                                deleteReferences = confirmDelete();
+
+                            if( deleteReferences.value() )
+                                nested_files->RemoveFile( name, true );
+                        }
+                    } );
+        }
+
+        if( deleteReferences.has_value() && deleteReferences.value() == false )
+            break;
+    }
+
     m_files->ClearEmbeddedFiles();
 
     std::vector<EMBEDDED_FILES::EMBEDDED_FILE*> files;
diff --git a/eeschema/schematic.cpp b/eeschema/schematic.cpp
index b58f69c34f..a826d1018b 100644
--- a/eeschema/schematic.cpp
+++ b/eeschema/schematic.cpp
@@ -936,6 +936,18 @@ const EMBEDDED_FILES* SCHEMATIC::GetEmbeddedFiles() const
 }
 
 
+void SCHEMATIC::RunOnNestedEmbeddedFiles( const std::function<void( EMBEDDED_FILES* )>& aFunction )
+{
+    SCH_SCREENS screens( Root() );
+
+    for( SCH_SCREEN* screen = screens.GetFirst(); screen; screen = screens.GetNext() )
+    {
+        for( auto& [name, libSym] : screen->GetLibSymbols() )
+            aFunction( libSym->GetEmbeddedFiles() );
+    }
+}
+
+
 std::set<KIFONT::OUTLINE_FONT*> SCHEMATIC::GetFonts() const
 {
     std::set<KIFONT::OUTLINE_FONT*> fonts;
diff --git a/eeschema/schematic.h b/eeschema/schematic.h
index d6b20e1fb8..f440586e5b 100644
--- a/eeschema/schematic.h
+++ b/eeschema/schematic.h
@@ -379,6 +379,8 @@ public:
      */
     void RemoveAllListeners();
 
+    void RunOnNestedEmbeddedFiles( const std::function<void( EMBEDDED_FILES* )>& aFunction ) override;
+
     /**
      * Embed fonts in the schematic.
      */
diff --git a/include/embedded_files.h b/include/embedded_files.h
index fa853ed930..1c7e08d8ca 100644
--- a/include/embedded_files.h
+++ b/include/embedded_files.h
@@ -175,6 +175,14 @@ public:
         return m_files.empty();
     }
 
+    /**
+     * Provide access to nested embedded files, such as symbols in schematics and footprints in
+     * boards.
+     */
+    virtual void RunOnNestedEmbeddedFiles( const std::function<void( EMBEDDED_FILES* )>& aFunction )
+    {
+    }
+
     /**
      * Helper function to get a list of fonts for fontconfig to add to the library.
      *
diff --git a/pcbnew/board.cpp b/pcbnew/board.cpp
index 3e17d8b324..f72e798357 100644
--- a/pcbnew/board.cpp
+++ b/pcbnew/board.cpp
@@ -1116,23 +1116,31 @@ void BOARD::CacheTriangulation( PROGRESS_REPORTER* aReporter, const std::vector<
 }
 
 
-void BOARD::FixupEmbeddedData()
+void BOARD::RunOnNestedEmbeddedFiles( const std::function<void( EMBEDDED_FILES* )>& aFunction )
 {
     for( FOOTPRINT* footprint : m_footprints )
-    {
-        for( auto& [filename, embeddedFile] : footprint->EmbeddedFileMap() )
-        {
-            EMBEDDED_FILES::EMBEDDED_FILE* file = GetEmbeddedFile( filename );
+        aFunction( footprint->GetEmbeddedFiles() );
+}
 
-            if( file )
+
+void BOARD::FixupEmbeddedData()
+{
+    RunOnNestedEmbeddedFiles(
+            [&]( EMBEDDED_FILES* nested )
             {
-                embeddedFile->compressedEncodedData = file->compressedEncodedData;
-                embeddedFile->decompressedData = file->decompressedData;
-                embeddedFile->data_hash = file->data_hash;
-                embeddedFile->is_valid = file->is_valid;
-            }
-        }
-    }
+                for( auto& [filename, embeddedFile] : nested->EmbeddedFileMap() )
+                {
+                    EMBEDDED_FILES::EMBEDDED_FILE* file = GetEmbeddedFile( filename );
+
+                    if( file )
+                    {
+                        embeddedFile->compressedEncodedData = file->compressedEncodedData;
+                        embeddedFile->decompressedData = file->decompressedData;
+                        embeddedFile->data_hash = file->data_hash;
+                        embeddedFile->is_valid = file->is_valid;
+                    }
+                }
+            } );
 }
 
 
diff --git a/pcbnew/board.h b/pcbnew/board.h
index 375be9815c..2ac10df4d1 100644
--- a/pcbnew/board.h
+++ b/pcbnew/board.h
@@ -474,6 +474,8 @@ public:
     */
     void FixupEmbeddedData();
 
+    void RunOnNestedEmbeddedFiles( const std::function<void( EMBEDDED_FILES* )>& aFunction ) override;
+
     void CacheTriangulation( PROGRESS_REPORTER* aReporter = nullptr,
                              const std::vector<ZONE*>& aZones = {} );