diff --git a/rpcs3/Emu/RSX/rsx_cache.h b/rpcs3/Emu/RSX/rsx_cache.h
index 6fedcf5753c9..07098dbb2f20 100644
--- a/rpcs3/Emu/RSX/rsx_cache.h
+++ b/rpcs3/Emu/RSX/rsx_cache.h
@@ -447,17 +447,31 @@ namespace rsx
 					fs::dir_entry tmp = entries[pos];
 
 					const auto filename = directory_path + "/" + tmp.name;
-					std::vector<u8> bytes;
 					fs::file f(filename);
+
+					if (!f)
+					{
+						// Unexpected error, but avoid crash
+						continue;
+					}
+
 					if (f.size() != sizeof(pipeline_data))
 					{
 						rsx_log.error("Removing cached pipeline object %s since it's not binary compatible with the current shader cache", tmp.name.c_str());
 						fs::remove_file(filename);
 						continue;
 					}
-					f.read<u8>(bytes, f.size());
 
-					auto entry = unpack(*reinterpret_cast<pipeline_data*>(bytes.data()));
+					pipeline_data pdata{};
+					f.read(&pdata, f.size();
+
+					auto entry = unpack(pdata);
+
+					if (std::get<1>(entry).data.empty() || !std::get<2>(entry).ucode_length)
+					{
+						continue;
+					}
+
 					m_storage.preload_programs(std::get<1>(entry), std::get<2>(entry));
 
 					unpacked[unpacked.push_begin()] = entry;
@@ -573,23 +587,22 @@ namespace rsx
 
 			std::string directory_path = root_path + "/pipelines/" + pipeline_class_name + "/" + version_prefix;
 
-			if (!fs::is_dir(directory_path))
+			fs::dir root = fs::dir(directory_path);
+
+			if (!root)
 			{
 				fs::create_path(directory_path);
 				fs::create_path(root_path + "/raw");
-
 				return;
 			}
 
-			fs::dir root = fs::dir(directory_path);
-
 			u32 entry_count = 0;
 			std::vector<fs::dir_entry> entries;
 			for (auto It = root.begin(); It != root.end(); ++It, entry_count++)
 			{
 				fs::dir_entry tmp = *It;
 
-				if (tmp.name == "." || tmp.name == "..")
+				if (tmp.is_directory || tmp.name.ends_with(".temp"))
 					continue;
 
 				entries.push_back(tmp);
@@ -648,12 +661,16 @@ namespace rsx
 
 			if (!fs::is_file(fp_name))
 			{
-				fs::file(fp_name, fs::rewrite).write(fp.get_data(), fp.ucode_length);
+				const std::string temp_name = fmt::format("%s.%s.temp", fp_name, fmt::base57(utils::get_unique_tsc()));
+				fs::file(temp_name, fs::rewrite).write(fp.get_data(), fp.ucode_length);
+				fs::rename(temp_name, fp_name, true); // Atomically write data
 			}
 
 			if (!fs::is_file(vp_name))
 			{
-				fs::file(vp_name, fs::rewrite).write<u32>(vp.data);
+				const std::string temp_name = fmt::format("%s.%s.temp", vp_name, fmt::base57(utils::get_unique_tsc()));
+				fs::file(temp_name, fs::rewrite).write(vp.data);
+				fs::rename(temp_name, fp_name, true); // Atomically write data
 			}
 
 			u64 state_hash = 0;
@@ -669,21 +686,22 @@ namespace rsx
 			state_hash ^= rpcs3::hash_base<u16>(data.fp_shadow_textures);
 			state_hash ^= rpcs3::hash_base<u16>(data.fp_redirected_textures);
 
-			std::string pipeline_file_name = fmt::format("%llX+%llX+%llX+%llX.bin", data.vertex_program_hash, data.fragment_program_hash, data.pipeline_storage_hash, state_hash);
-			std::string pipeline_path = root_path + "/pipelines/" + pipeline_class_name + "/" + version_prefix + "/" + pipeline_file_name;
-			fs::file(pipeline_path, fs::rewrite).write(&data, sizeof(pipeline_data));
+			const std::string pipeline_file_name = fmt::format("%llX+%llX+%llX+%llX.bin", data.vertex_program_hash, data.fragment_program_hash, data.pipeline_storage_hash, state_hash);
+			const std::string pipeline_path = root_path + "/pipelines/" + pipeline_class_name + "/" + version_prefix + "/" + pipeline_file_name;
+			const std::string temp_path = fmt::format("%s.%s.temp", pipeline_path, fmt::base57(utils::get_unique_tsc()));
+			fs::file(temp_path, fs::rewrite).write(&data, sizeof(data));
+			fs::rename(temp_path, pipeline_path, true);
 		}
 
 		RSXVertexProgram load_vp_raw(u64 program_hash)
 		{
-			std::vector<u32> data;
+			RSXVertexProgram vp = {};
+
 			std::string filename = fmt::format("%llX.vp", program_hash);
 
 			fs::file f(root_path + "/raw/" + filename);
-			f.read<u32>(data, f.size() / sizeof(u32));
+			if (f) f.read(vp.data, f.size() / sizeof(u32));
 
-			RSXVertexProgram vp = {};
-			vp.data = data;
 			vp.skip_vertex_input_check = true;
 
 			return vp;
@@ -695,15 +713,15 @@ namespace rsx
 			std::string filename = fmt::format("%llX.fp", program_hash);
 
 			fs::file f(root_path + "/raw/" + filename);
-			f.read<u8>(data, f.size());
+			if (f) f.read(data, f.size() / sizeof(u32));
 
 			RSXFragmentProgram fp = {};
+			fp.ucode_length = ::size32(data);
 			{
-				std::lock_guard<std::mutex> lock(fpd_mutex);
-				fragment_program_data[program_hash] = data;
+				std::lock_guard lock(fpd_mutex);
+				fragment_program_data.insert_or_assign(program_hash, std::move(data));
 				fp.data = fragment_program_data[program_hash].data();
 			}
-			fp.ucode_length = ::size32(data);
 
 			return fp;
 		}