diff --git a/Source/Core/UICommon/CommandLineParse.cpp b/Source/Core/UICommon/CommandLineParse.cpp
index e591a2accf..0fe4a0c0d4 100644
--- a/Source/Core/UICommon/CommandLineParse.cpp
+++ b/Source/Core/UICommon/CommandLineParse.cpp
@@ -2,13 +2,65 @@
 // Licensed under GPLv2+
 // Refer to the license.txt file included.
 
+#include <list>
+#include <sstream>
+#include <string>
+#include <tuple>
+
 #include <OptionParser.h>
 
 #include "Common/Common.h"
+#include "Common/Config/Config.h"
 #include "UICommon/CommandLineParse.h"
 
 namespace CommandLineParse
 {
+class CommandLineConfigLayerLoader final : public Config::ConfigLayerLoader
+{
+public:
+  CommandLineConfigLayerLoader(const std::list<std::string>& args, const std::string& video_backend,
+                               const std::string& audio_backend)
+      : ConfigLayerLoader(Config::LayerType::CommandLine)
+  {
+    if (video_backend.size())
+      m_values.emplace_back(std::make_tuple("Dolphin", "Core", "GFXBackend", video_backend));
+
+    if (audio_backend.size())
+      m_values.emplace_back(
+          std::make_tuple("Dolphin", "Core", "DSPHLE", audio_backend == "HLE" ? "True" : "False"));
+
+    // Arguments are in the format of <System>.<Section>.<Key>=Value
+    for (const auto& arg : args)
+    {
+      std::istringstream buffer(arg);
+      std::string system, section, key, value;
+      std::getline(buffer, system, '.');
+      std::getline(buffer, section, '.');
+      std::getline(buffer, key, '=');
+      std::getline(buffer, value, '=');
+      m_values.emplace_back(std::make_tuple(system, section, key, value));
+    }
+  }
+
+  void Load(Config::Layer* config_layer) override
+  {
+    for (auto& value : m_values)
+    {
+      Config::Section* section = config_layer->GetOrCreateSection(
+          Config::GetSystemFromName(std::get<0>(value)), std::get<1>(value));
+      section->Set(std::get<2>(value), std::get<3>(value));
+    }
+  }
+
+  void Save(Config::Layer* config_layer) override
+  {
+    // Save Nothing
+  }
+
+private:
+  std::list<std::tuple<std::string, std::string, std::string, std::string>> m_values;
+};
+
 std::unique_ptr<optparse::OptionParser> CreateParser(ParserOptions options)
 {
   auto parser = std::make_unique<optparse::OptionParser>();
@@ -23,6 +75,11 @@ std::unique_ptr<optparse::OptionParser> CreateParser(ParserOptions options)
       .metavar("<file>")
       .type("string")
       .help("Load the specified file");
+  parser->add_option("-C", "--config")
+      .action("append")
+      .metavar("<System>.<Section>.<Key>=<Value>")
+      .type("string")
+      .help("Set a configuration option");
 
   if (options == ParserOptions::IncludeGUIOptions)
   {
@@ -32,7 +89,8 @@ std::unique_ptr<optparse::OptionParser> CreateParser(ParserOptions options)
     parser->add_option("-c", "--confirm").action("store_true").help("Set Confirm on Stop");
   }
 
-  // XXX: These two are setting configuration options
+  parser->set_defaults("video_backend", "");
+  parser->set_defaults("audio_emulation", "");
   parser->add_option("-v", "--video_backend").action("store").help("Specify a video backend");
   parser->add_option("-a", "--audio_emulation")
       .choices({"HLE", "LLE"})
@@ -43,6 +101,15 @@ std::unique_ptr<optparse::OptionParser> CreateParser(ParserOptions options)
 
 optparse::Values& ParseArguments(optparse::OptionParser* parser, int argc, char** argv)
 {
-  return parser->parse_args(argc, argv);
+  optparse::Values& options = parser->parse_args(argc, argv);
+
+  const std::list<std::string>& config_args = options.all("config");
+  if (config_args.size())
+  {
+    Config::AddLayer(std::make_unique<CommandLineConfigLayerLoader>(
+        config_args, static_cast<const char*>(options.get("video_backend")),
+        static_cast<const char*>(options.get("audio_emulation"))));
+  }
+  return options;
 }
 }