diff --git a/Source/Core/Core/Boot/Boot.cpp b/Source/Core/Core/Boot/Boot.cpp
index 86ea8e2179..94b66bd687 100644
--- a/Source/Core/Core/Boot/Boot.cpp
+++ b/Source/Core/Core/Boot/Boot.cpp
@@ -701,7 +701,8 @@ void AddRiivolutionPatches(BootParameters* boot_params,
   disc.volume = DiscIO::CreateDisc(DiscIO::DirectoryBlobReader::Create(
       std::move(disc.volume),
       [&](std::vector<DiscIO::FSTBuilderNode>* fst, DiscIO::FSTBuilderNode* dol_node) {
-        DiscIO::Riivolution::ApplyPatchesToFiles(riivolution_patches, fst, dol_node);
+        DiscIO::Riivolution::ApplyPatchesToFiles(
+            riivolution_patches, DiscIO::Riivolution::PatchIndex::FileSystem, fst, dol_node);
       }));
   boot_params->riivolution_patches = std::move(riivolution_patches);
 }
diff --git a/Source/Core/DiscIO/RiivolutionParser.cpp b/Source/Core/DiscIO/RiivolutionParser.cpp
index 283e5876df..dacbbbcfc5 100644
--- a/Source/Core/DiscIO/RiivolutionParser.cpp
+++ b/Source/Core/DiscIO/RiivolutionParser.cpp
@@ -172,9 +172,10 @@ std::optional<Disc> ParseString(std::string_view xml, std::string xml_path)
     for (const auto& patch_subnode : patch_node.children())
     {
       const std::string_view patch_name(patch_subnode.name());
-      if (patch_name == "file")
+      if (patch_name == "file" || patch_name == "dolphin_sys_file")
       {
-        auto& file = patch.m_file_patches.emplace_back();
+        auto& file = patch_name == "dolphin_sys_file" ? patch.m_sys_file_patches.emplace_back() :
+                                                        patch.m_file_patches.emplace_back();
         file.m_disc = patch_subnode.attribute("disc").as_string();
         file.m_external = patch_subnode.attribute("external").as_string();
         file.m_resize = patch_subnode.attribute("resize").as_bool(true);
@@ -183,9 +184,11 @@ std::optional<Disc> ParseString(std::string_view xml, std::string xml_path)
         file.m_fileoffset = patch_subnode.attribute("fileoffset").as_uint(0);
         file.m_length = patch_subnode.attribute("length").as_uint(0);
       }
-      else if (patch_name == "folder")
+      else if (patch_name == "folder" || patch_name == "dolphin_sys_folder")
       {
-        auto& folder = patch.m_folder_patches.emplace_back();
+        auto& folder = patch_name == "dolphin_sys_folder" ?
+                           patch.m_sys_folder_patches.emplace_back() :
+                           patch.m_folder_patches.emplace_back();
         folder.m_disc = patch_subnode.attribute("disc").as_string();
         folder.m_external = patch_subnode.attribute("external").as_string();
         folder.m_resize = patch_subnode.attribute("resize").as_bool(true);
diff --git a/Source/Core/DiscIO/RiivolutionParser.h b/Source/Core/DiscIO/RiivolutionParser.h
index f9f03f67c1..9ec6c92959 100644
--- a/Source/Core/DiscIO/RiivolutionParser.h
+++ b/Source/Core/DiscIO/RiivolutionParser.h
@@ -166,6 +166,8 @@ struct Patch
 
   std::vector<File> m_file_patches;
   std::vector<Folder> m_folder_patches;
+  std::vector<File> m_sys_file_patches;
+  std::vector<Folder> m_sys_folder_patches;
   std::vector<Savegame> m_savegame_patches;
   std::vector<Memory> m_memory_patches;
 
diff --git a/Source/Core/DiscIO/RiivolutionPatcher.cpp b/Source/Core/DiscIO/RiivolutionPatcher.cpp
index a9593dddcd..8ad65f8c57 100644
--- a/Source/Core/DiscIO/RiivolutionPatcher.cpp
+++ b/Source/Core/DiscIO/RiivolutionPatcher.cpp
@@ -458,15 +458,20 @@ static void ApplyFolderPatchToFST(const Patch& patch, const Folder& folder,
   ApplyFolderPatchToFST(patch, folder, fst, dol_node, folder.m_disc, folder.m_external);
 }
 
-void ApplyPatchesToFiles(const std::vector<Patch>& patches,
+void ApplyPatchesToFiles(const std::vector<Patch>& patches, PatchIndex index,
                          std::vector<DiscIO::FSTBuilderNode>* fst, DiscIO::FSTBuilderNode* dol_node)
 {
   for (const auto& patch : patches)
   {
-    for (const auto& file : patch.m_file_patches)
+    const auto& file_patches =
+        index == PatchIndex::DolphinSysFiles ? patch.m_sys_file_patches : patch.m_file_patches;
+    const auto& folder_patches =
+        index == PatchIndex::DolphinSysFiles ? patch.m_sys_folder_patches : patch.m_folder_patches;
+
+    for (const auto& file : file_patches)
       ApplyFilePatchToFST(patch, file, fst, dol_node);
 
-    for (const auto& folder : patch.m_folder_patches)
+    for (const auto& folder : folder_patches)
       ApplyFolderPatchToFST(patch, folder, fst, dol_node);
   }
 }
diff --git a/Source/Core/DiscIO/RiivolutionPatcher.h b/Source/Core/DiscIO/RiivolutionPatcher.h
index 0f3de33caf..0a83ba9d13 100644
--- a/Source/Core/DiscIO/RiivolutionPatcher.h
+++ b/Source/Core/DiscIO/RiivolutionPatcher.h
@@ -65,7 +65,13 @@ private:
   std::string m_patch_root;
 };
 
-void ApplyPatchesToFiles(const std::vector<Patch>& patches,
+enum class PatchIndex
+{
+  FileSystem,
+  DolphinSysFiles,
+};
+
+void ApplyPatchesToFiles(const std::vector<Patch>& patches, PatchIndex index,
                          std::vector<DiscIO::FSTBuilderNode>* fst,
                          DiscIO::FSTBuilderNode* dol_node);
 void ApplyGeneralMemoryPatches(const std::vector<Patch>& patches);