diff --git a/src/storm/settings/Option.cpp b/src/storm/settings/Option.cpp
index 1ab2aa23a..99d03aede 100644
--- a/src/storm/settings/Option.cpp
+++ b/src/storm/settings/Option.cpp
@@ -117,8 +117,12 @@ namespace storm {
 			bool Option::getHasOptionBeenSet() const {
 				return this->hasBeenSet;
 			}
+   
+			bool Option::getHasOptionBeenSetWithModulePrefix() const {
+				return this->hasBeenSetWithModulePrefix;
+			}
 
-            Option::Option(std::string const& moduleName, std::string const& longOptionName, std::string const& shortOptionName, bool hasShortOptionName, std::string const& optionDescription, bool isOptionRequired, bool requireModulePrefix, bool isAdvanced, std::vector<std::shared_ptr<ArgumentBase>> const& optionArguments) : longName(longOptionName), hasShortName(hasShortOptionName), shortName(shortOptionName), description(optionDescription), moduleName(moduleName), isRequired(isOptionRequired), requireModulePrefix(requireModulePrefix), isAdvanced(isAdvanced), hasBeenSet(false), arguments(optionArguments), argumentNameMap() {
+            Option::Option(std::string const& moduleName, std::string const& longOptionName, std::string const& shortOptionName, bool hasShortOptionName, std::string const& optionDescription, bool isOptionRequired, bool requireModulePrefix, bool isAdvanced, std::vector<std::shared_ptr<ArgumentBase>> const& optionArguments) : longName(longOptionName), hasShortName(hasShortOptionName), shortName(shortOptionName), description(optionDescription), moduleName(moduleName), isRequired(isOptionRequired), requireModulePrefix(requireModulePrefix), isAdvanced(isAdvanced), hasBeenSet(false), hasBeenSetWithModulePrefix(false), arguments(optionArguments), argumentNameMap() {
                 // First, do some sanity checks.
                 STORM_LOG_THROW(!longName.empty(), storm::exceptions::IllegalArgumentException, "Unable to construct option with empty name.");
                 STORM_LOG_THROW(!moduleName.empty(), storm::exceptions::IllegalArgumentException, "Unable to construct option with empty module name.");
@@ -138,6 +142,10 @@ namespace storm {
             void  Option::setHasOptionBeenSet(bool newValue) {
                 this->hasBeenSet = newValue;
             }
+            
+            void  Option::setHasOptionBeenSetWithModulePrefix(bool newValue) {
+                this->hasBeenSetWithModulePrefix = newValue;
+            }
         
             uint_fast64_t Option::getPrintLength() const {
                 uint_fast64_t length = 2;
diff --git a/src/storm/settings/Option.h b/src/storm/settings/Option.h
index 0ff675d21..926dad8d9 100644
--- a/src/storm/settings/Option.h
+++ b/src/storm/settings/Option.h
@@ -161,6 +161,13 @@ namespace storm {
              * @return True iff the option has been set.
              */
             bool getHasOptionBeenSet() const;
+            
+            /*!
+             * Retrieves whether the option has been set by including the module prefix.
+             *
+             * @return True iff the option has been set by including the module prefix.
+             */
+            bool getHasOptionBeenSetWithModulePrefix() const;
 
             /*!
              * Retrieves whether the option is only displayed in the advanced help.
@@ -210,6 +217,9 @@ namespace storm {
             
             // A flag that indicates whether this option has been set.
             bool hasBeenSet;
+            
+            // A flag that indicates whether this option has been set.
+            bool hasBeenSetWithModulePrefix;
 
             // The arguments of this option (possibly empty).
             std::vector<std::shared_ptr<ArgumentBase>> arguments;
@@ -239,6 +249,13 @@ namespace storm {
              * @param newValue The new status of the flag.
              */
             void setHasOptionBeenSet(bool newValue = true);
+            
+            /*!
+             * Sets the flag that marks the option as being (un)set by including the module prefix.
+             *
+             * @param newValue The new status of the flag.
+             */
+            void setHasOptionBeenSetWithModulePrefix(bool newValue = true);
 		};
 	}
 }
diff --git a/src/storm/settings/SettingsManager.cpp b/src/storm/settings/SettingsManager.cpp
index 04cb48621..f3b9009b2 100644
--- a/src/storm/settings/SettingsManager.cpp
+++ b/src/storm/settings/SettingsManager.cpp
@@ -494,6 +494,9 @@ namespace storm {
             }
             
             option->setHasOptionBeenSet();
+            if (optionName != option->getLongName() && optionName != option->getShortName() && boost::starts_with(optionName, option->getModuleName())) {
+                option->setHasOptionBeenSetWithModulePrefix();
+            }
         }
         
         void SettingsManager::setOptionsArguments(std::string const& optionName, std::unordered_map<std::string, std::vector<std::shared_ptr<Option>>> const& optionMap, std::vector<std::string> const& argumentCache) {
diff --git a/src/storm/settings/modules/ModuleSettings.cpp b/src/storm/settings/modules/ModuleSettings.cpp
index 528535ec2..b9dde8b08 100644
--- a/src/storm/settings/modules/ModuleSettings.cpp
+++ b/src/storm/settings/modules/ModuleSettings.cpp
@@ -26,6 +26,7 @@ namespace storm {
             
             void ModuleSettings::unset(std::string const& name) {
                 return this->getOption(name).setHasOptionBeenSet(false);
+                return this->getOption(name).setHasOptionBeenSetWithModulePrefix(false);
             }
             
             std::vector<std::shared_ptr<Option>> const& ModuleSettings::getOptions() const {