diff --git a/src/core/file_sys/ncch_container.cpp b/src/core/file_sys/ncch_container.cpp
index 5efd5e54de..cf050e74e3 100644
--- a/src/core/file_sys/ncch_container.cpp
+++ b/src/core/file_sys/ncch_container.cpp
@@ -539,26 +539,28 @@ Loader::ResultStatus NCCHContainer::LoadSectionExeFS(const char* name, std::vect
                 }
             }
 
-            std::string override_ips = filepath + ".exefsdir/code.ips";
-
-            if (FileUtil::Exists(override_ips) && strcmp(name, ".code") == 0) {
-                FileUtil::IOFile ips_file(override_ips, "rb");
-                std::size_t ips_file_size = ips_file.GetSize();
-                std::vector<u8> ips(ips_file_size);
-
-                if (ips_file.IsOpen() &&
-                    ips_file.ReadBytes(&ips[0], ips_file_size) == ips_file_size) {
-                    LOG_INFO(Service_FS, "File {} patching code.bin", override_ips);
-                    ApplyIPS(ips, buffer);
-                }
-            }
-
             return Loader::ResultStatus::Success;
         }
     }
     return Loader::ResultStatus::ErrorNotUsed;
 }
 
+bool NCCHContainer::ApplyIPSPatch(std::vector<u8>& code) const {
+    const std::string override_ips = filepath + ".exefsdir/code.ips";
+
+    FileUtil::IOFile ips_file{override_ips, "rb"};
+    if (!ips_file)
+        return false;
+
+    std::vector<u8> ips(ips_file.GetSize());
+    if (ips_file.ReadBytes(ips.data(), ips.size()) != ips.size())
+        return false;
+
+    LOG_INFO(Service_FS, "File {} patching code.bin", override_ips);
+    ApplyIPS(ips, code);
+    return true;
+}
+
 Loader::ResultStatus NCCHContainer::LoadOverrideExeFSSection(const char* name,
                                                              std::vector<u8>& buffer) {
     std::string override_name;
diff --git a/src/core/file_sys/ncch_container.h b/src/core/file_sys/ncch_container.h
index 89a2d12898..00d44c8180 100644
--- a/src/core/file_sys/ncch_container.h
+++ b/src/core/file_sys/ncch_container.h
@@ -271,6 +271,13 @@ public:
      */
     Loader::ResultStatus ReadExtdataId(u64& extdata_id);
 
+    /**
+     * Apply an IPS patch for .code (if it exists).
+     * This should only be called after allocating .bss.
+     * @return bool true if a patch was applied, false otherwise
+     */
+    bool ApplyIPSPatch(std::vector<u8>& code) const;
+
     /**
      * Checks whether the NCCH container contains an ExeFS
      * @return bool check result
diff --git a/src/core/loader/ncch.cpp b/src/core/loader/ncch.cpp
index 9ece9c69e9..286eadaab2 100644
--- a/src/core/loader/ncch.cpp
+++ b/src/core/loader/ncch.cpp
@@ -100,6 +100,9 @@ ResultStatus AppLoader_NCCH::LoadExec(std::shared_ptr<Kernel::Process>& process)
             overlay_ncch->exheader_header.codeset_info.data.num_max_pages * Memory::PAGE_SIZE +
             bss_page_size;
 
+        // Apply any IPS patch now that the entire codeset (including .bss) has been allocated
+        overlay_ncch->ApplyIPSPatch(code);
+
         codeset->entrypoint = codeset->CodeSegment().addr;
         codeset->memory = std::move(code);