diff --git a/src/app/app.cpp b/src/app/app.cpp
index 4f73ae16..54a14d07 100644
--- a/src/app/app.cpp
+++ b/src/app/app.cpp
@@ -520,7 +520,9 @@ bool CApplication::Create()
         GetLogger()->Warn("Config could not be loaded. Default values will be used!\n");
     }
 
-    m_modManager->ReinitMods();
+    m_modManager->FindMods();
+    m_modManager->SaveMods();
+    m_modManager->UpdatePaths();
 
     // Create the sound instance.
     #ifdef OPENAL_SOUND
diff --git a/src/app/modman.cpp b/src/app/modman.cpp
index b67853ce..ef044a8a 100644
--- a/src/app/modman.cpp
+++ b/src/app/modman.cpp
@@ -19,22 +19,18 @@
 
 #include "app/modman.h"
 
-//TODO: clean up includes
 #include "common/config.h"
 
 #include "app/app.h"
 #include "app/pathman.h"
 
+#include "common/config_file.h"
 #include "common/logger.h"
-#include "common/restext.h"
-#include "common/settings.h"
-#include "common/stringutils.h"
 
 #include "common/resources/resourcemanager.h"
 
-#include "common/system/system.h"
-
 #include <algorithm>
+#include <set>
 #include <boost/filesystem.hpp>
 #include <boost/algorithm/string.hpp>
 
@@ -46,16 +42,64 @@ CModManager::CModManager(CApplication* app, CPathManager* pathManager)
 {
 }
 
-void CModManager::ReinitMods()
+void CModManager::FindMods()
 {
     m_mods.clear();
-    const auto foundMods = m_pathManager->FindMods();
-    for (const auto& modPath : foundMods)
+
+    // Load names from the config file
+    std::vector<std::string> savedModNames;
+    GetConfigFile().GetArrayProperty("Mods", "Names", savedModNames);
+    std::vector<bool> savedEnabled;
+    GetConfigFile().GetArrayProperty("Mods", "Enabled", savedEnabled);
+
+    // Transform the data into Mod structures
+    m_mods.reserve(savedModNames.size());
+    for (int i = 0; i < savedModNames.size(); ++i)
     {
-        Mod mod;
-        mod.name = boost::filesystem::path(modPath).stem().string();
-        mod.path = modPath;
-        mod.enabled = m_pathManager->ModLoaded(mod.path); //TODO: load from some config file
+        Mod mod{};
+        mod.name = savedModNames[i];
+        if (i < savedEnabled.size())
+        {
+            mod.enabled = savedEnabled[i];
+        }
+        mod.path = ""; // Find the path later
+        m_mods.push_back(mod);
+    }
+
+    // Search the folders for mods
+    const auto rawPaths = m_pathManager->FindMods();
+    std::map<std::string, std::string> modPaths;
+    for (const auto& path : rawPaths)
+    {
+        auto modName = boost::filesystem::path(path).stem().string();
+        modPaths.insert(std::make_pair(modName, path));
+    }
+
+    // Find paths for already saved mods
+    auto it = m_mods.begin();
+    while (it != m_mods.end())
+    {
+        auto& mod = *it;
+        const auto pathsIt = modPaths.find(mod.name);
+        if (pathsIt != modPaths.end())
+        {
+            mod.path = (*pathsIt).second;
+            modPaths.erase(pathsIt);
+            ++it;
+        }
+        else
+        {
+            GetLogger()->Warn("Could not find mod %s, removing it from the list\n", mod.name.c_str());
+            it = m_mods.erase(it);
+        }
+    }
+
+    // Add the remaining found mods to the end of the list
+    for (const auto& newMod : modPaths)
+    {
+        Mod mod{};
+        mod.name = newMod.first;
+        mod.path = newMod.second;
         m_mods.push_back(mod);
     }
 }
@@ -82,23 +126,38 @@ void CModManager::DisableMod(const std::string& modName)
     mod->enabled = false;
 }
 
-void CModManager::ReloadMods()
+void CModManager::UpdatePaths()
 {
+    m_pathManager->RemoveAllMods();
     for (const auto& mod : m_mods)
     {
-        bool loaded = m_pathManager->ModLoaded(mod.path);
-        if (mod.enabled && !loaded)
+        if (mod.enabled)
         {
             m_pathManager->AddMod(mod.path);
         }
-        else if (!mod.enabled && loaded)
-        {
-            m_pathManager->RemoveMod(mod.path);
-        }
     }
+}
+
+void CModManager::ReloadResources()
+{
     m_app->ReloadResources();
 }
 
+void CModManager::SaveMods()
+{
+    std::vector<std::string> savedNames;
+    savedNames.reserve(m_mods.size());
+    std::transform(m_mods.begin(), m_mods.end(), std::back_inserter(savedNames), [](const Mod& mod) { return mod.name; });
+    GetConfigFile().SetArrayProperty("Mods", "Names", savedNames);
+
+    std::vector<bool> savedEnabled;
+    savedEnabled.reserve(m_mods.size());
+    std::transform(m_mods.begin(), m_mods.end(), std::back_inserter(savedEnabled), [](const Mod& mod) { return mod.enabled; });
+    GetConfigFile().SetArrayProperty("Mods", "Enabled", savedEnabled);
+
+    GetConfigFile().Save();
+}
+
 boost::optional<Mod> CModManager::GetMod(const std::string& modName)
 {
     Mod* mod = FindMod(modName);
diff --git a/src/app/modman.h b/src/app/modman.h
index e1a47467..5ce3efa2 100644
--- a/src/app/modman.h
+++ b/src/app/modman.h
@@ -30,8 +30,8 @@ class CPathManager;
 
 struct Mod
 {
-    std::string name;
-    std::string path;
+    std::string name{};
+    std::string path{};
     bool enabled = false;
     //TODO: add metadata for UI
 };
@@ -41,6 +41,7 @@ struct Mod
  * \brief Main application
  *
  * This class handles the list of currently loaded mods.
+ * The order matters since the order in which files are loaded matters.
  *
  */
 class CModManager
@@ -49,7 +50,7 @@ public:
     CModManager(CApplication* app, CPathManager* pathManager);
 
     //! Finds all the mods along with their metadata
-    void ReinitMods();
+    void FindMods();
 
     //! Removes a mod from the list of loaded mods
     void EnableMod(const std::string& modName);
@@ -58,7 +59,13 @@ public:
     void DisableMod(const std::string& modName);
 
     //! Reloads application resources so the enabled mods are applied
-    void ReloadMods();
+    void ReloadResources();
+
+    //! Saves the current configuration of mods to the config file
+    void SaveMods();
+
+    //! Updates the paths in Path Manager according to the current mod configuration
+    void UpdatePaths();
 
     boost::optional<Mod> GetMod(const std::string& modName);
     const std::vector<Mod>& GetMods() const;
diff --git a/src/app/pathman.cpp b/src/app/pathman.cpp
index 4c4a1a71..080c9b70 100644
--- a/src/app/pathman.cpp
+++ b/src/app/pathman.cpp
@@ -73,17 +73,30 @@ void CPathManager::AddMod(const std::string &modPath)
 {
     GetLogger()->Info("Loading mod: '%s'\n", modPath.c_str());
     CResourceManager::AddLocation(modPath, true);
+    m_mods.push_back(modPath);
 }
 
 void CPathManager::RemoveMod(const std::string &modPath)
 {
     GetLogger()->Info("Unloading mod: '%s'\n", modPath.c_str());
     CResourceManager::RemoveLocation(modPath);
+    auto it = std::find(m_mods.cbegin(), m_mods.cend(), modPath);
+    if (it != m_mods.cend())
+        m_mods.erase(it);
+}
+
+void CPathManager::RemoveAllMods()
+{
+    for (const auto& modPath : m_mods)
+    {
+        CResourceManager::RemoveLocation(modPath);
+    }
+    m_mods.clear();
 }
 
 bool CPathManager::ModLoaded(const std::string& modPath)
 {
-    return CResourceManager::LocationExists(modPath);
+    return std::find(m_mods.cbegin(), m_mods.cend(), modPath) != m_mods.end();
 }
 
 std::vector<std::string> CPathManager::FindMods() const
diff --git a/src/app/pathman.h b/src/app/pathman.h
index 7726786d..2fedfee6 100644
--- a/src/app/pathman.h
+++ b/src/app/pathman.h
@@ -40,6 +40,7 @@ public:
     void AddModSearchDir(const std::string &modSearchDirPath);
     void AddMod(const std::string &modPath);
     void RemoveMod(const std::string &modPath);
+    void RemoveAllMods();
     bool ModLoaded(const std::string& modPath);
     std::vector<std::string> FindMods() const;
 
@@ -65,4 +66,6 @@ private:
     std::string m_savePath;
     //! Mod search paths
     std::vector<std::string> m_modSearchDirs;
+    //! Mod paths
+    std::vector<std::string> m_mods;
 };
diff --git a/src/ui/screen/screen_setup_mods.cpp b/src/ui/screen/screen_setup_mods.cpp
index 6fae8151..69cd13fe 100644
--- a/src/ui/screen/screen_setup_mods.cpp
+++ b/src/ui/screen/screen_setup_mods.cpp
@@ -71,6 +71,8 @@ void CScreenSetupMods::CreateInterface()
     Math::Point     pos, ddim;
     std::string     name;
 
+    m_modManager->FindMods();
+
     CScreenSetup::CreateInterface();
     pw = static_cast<CWindow*>(m_interface->SearchControl(EVENT_WINDOW5));
     if ( pw == nullptr )  return;
@@ -155,7 +157,9 @@ bool CScreenSetupMods::EventProcess(const Event &event)
             modName = pl->GetItemName(pl->GetSelect());
 
             m_modManager->EnableMod(modName);
-            m_modManager->ReloadMods();
+            m_modManager->SaveMods();
+            m_modManager->UpdatePaths();
+            m_modManager->ReloadResources();
 
             m_main->ChangePhase(PHASE_SETUPm);
             break;
@@ -166,7 +170,9 @@ bool CScreenSetupMods::EventProcess(const Event &event)
             modName = pl->GetItemName(pl->GetSelect());
 
             m_modManager->DisableMod(modName);
-            m_modManager->ReloadMods();
+            m_modManager->SaveMods();
+            m_modManager->UpdatePaths();
+            m_modManager->ReloadResources();
 
             m_main->ChangePhase(PHASE_SETUPm);
             break;