diff --git a/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.cpp b/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.cpp
index 38e8863befeee4dd9da76df3cbff9d6a408117c6..f9e0bf63d2ff1e8e119616983e36fb76be192cb8 100644
--- a/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.cpp
+++ b/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.cpp
@@ -222,9 +222,7 @@ std::string MainWindowPresenter::instrumentName() const {
 }
 
 void MainWindowPresenter::updateInstrument(const std::string &instrumentName) {
-  Mantid::Kernel::ConfigService::Instance().setString("default.instrument",
-                                                      instrumentName);
-  g_log.information() << "Instrument changed to " << instrumentName;
+  setDefaultInstrument(instrumentName);
 
   // Load a workspace for this instrument so we can get the actual instrument
   auto loadAlg =
@@ -246,6 +244,24 @@ void MainWindowPresenter::updateInstrument(const std::string &instrumentName) {
   m_slitCalculator->setCurrentInstrumentName(instrumentName);
   m_slitCalculator->processInstrumentHasBeenChanged();
 }
+
+void MainWindowPresenter::setDefaultInstrument(
+    const std::string &requiredInstrument) {
+  auto &config = Mantid::Kernel::ConfigService::Instance();
+
+  auto currentFacility = config.getString("default.facility");
+  auto requiredFacility = "ISIS";
+  if (currentFacility != requiredFacility) {
+    config.setString("default.facility", requiredFacility);
+    g_log.notice() << "Facility changed to " << requiredFacility;
+  }
+
+  auto currentInstrument = config.getString("default.instrument");
+  if (currentInstrument != requiredInstrument) {
+    config.setString("default.instrument", requiredInstrument);
+    g_log.notice() << "Instrument changed to " << requiredInstrument;
+  }
+}
 } // namespace ISISReflectometry
 } // namespace CustomInterfaces
 } // namespace MantidQt
diff --git a/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.h b/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.h
index 02d7e205ac3f95f003fd3f524966e89ab90fda3b..c1070a554bab67ee74248e476c961568e0879d03 100644
--- a/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.h
+++ b/qt/scientific_interfaces/ISISReflectometry/GUI/MainWindow/MainWindowPresenter.h
@@ -83,6 +83,7 @@ private:
                     std::string const &instrument);
   void changeInstrument(std::string const &instrumentName);
   void updateInstrument(const std::string &instrumentName);
+  void setDefaultInstrument(const std::string &newInstrument);
 
   void disableSaveAndLoadBatch();
   void enableSaveAndLoadBatch();
diff --git a/qt/scientific_interfaces/ISISReflectometry/GUI/RunsTable/QtRunsTableView.cpp b/qt/scientific_interfaces/ISISReflectometry/GUI/RunsTable/QtRunsTableView.cpp
index bf646821d4fb6a29f16f2aa9159de98a0e8d9034..607f5be498d08d9713e1c41c134e76499ac80376 100644
--- a/qt/scientific_interfaces/ISISReflectometry/GUI/RunsTable/QtRunsTableView.cpp
+++ b/qt/scientific_interfaces/ISISReflectometry/GUI/RunsTable/QtRunsTableView.cpp
@@ -6,7 +6,6 @@
 // SPDX - License - Identifier: GPL - 3.0 +
 #include "QtRunsTableView.h"
 #include "Common/IndexOf.h"
-#include "MantidKernel/ConfigService.h"
 #include "MantidKernel/UsageService.h"
 #include "MantidQtIcons/Icon.h"
 #include "MantidQtWidgets/Common/AlgorithmHintStrategy.h"
diff --git a/qt/scientific_interfaces/test/ISISReflectometry/MainWindow/MainWindowPresenterTest.h b/qt/scientific_interfaces/test/ISISReflectometry/MainWindow/MainWindowPresenterTest.h
index d0bf7862c3c68e554424f5faf32353284863f42e..a21fd3409a0fd5536d2ec488b420e54fc651898a 100644
--- a/qt/scientific_interfaces/test/ISISReflectometry/MainWindow/MainWindowPresenterTest.h
+++ b/qt/scientific_interfaces/test/ISISReflectometry/MainWindow/MainWindowPresenterTest.h
@@ -13,6 +13,7 @@
 #include "../ReflMockObjects.h"
 #include "MantidAPI/FrameworkManager.h"
 #include "MantidGeometry/Instrument_fwd.h"
+#include "MantidKernel/ConfigService.h"
 #include "MantidQtWidgets/Common/MockSlitCalculator.h"
 #include "MockMainWindowView.h"
 
@@ -49,6 +50,18 @@ public:
     ON_CALL(m_view, batches()).WillByDefault(Return(m_batchViews));
   }
 
+  void setUp() override {
+    auto &config = Mantid::Kernel::ConfigService::Instance();
+    backup_facility = config.getString("default.facility");
+    backup_instrument = config.getString("default.instrument");
+  }
+
+  void tearDown() override {
+    auto &config = Mantid::Kernel::ConfigService::Instance();
+    config.setString("default.facility", backup_facility);
+    config.setString("default.instrument", backup_instrument);
+  }
+
   void testPresenterSubscribesToView() {
     EXPECT_CALL(m_view, subscribe(_)).Times(1);
     auto presenter = makePresenter();
@@ -282,6 +295,26 @@ public:
     verifyAndClear();
   }
 
+  void testUpdateInstrumentSetsFacilityInConfig() {
+    auto presenter = makePresenter();
+    auto const instrument = setupInstrument(presenter, "POLREF");
+    auto &config = Mantid::Kernel::ConfigService::Instance();
+    config.setString("default.facility", "OLD_FACILITY");
+    presenter.notifyUpdateInstrumentRequested();
+    TS_ASSERT_EQUALS(config.getString("default.facility"), "ISIS");
+    verifyAndClear();
+  }
+
+  void testUpdateInstrumentSetsInstrumentInConfig() {
+    auto presenter = makePresenter();
+    auto const instrument = setupInstrument(presenter, "POLREF");
+    auto &config = Mantid::Kernel::ConfigService::Instance();
+    config.setString("default.instrument", "OLD_INSTRUMENT");
+    presenter.notifyUpdateInstrumentRequested();
+    TS_ASSERT_EQUALS(config.getString("default.instrument"), instrument);
+    verifyAndClear();
+  }
+
 private:
   NiceMock<MockMainWindowView> m_view;
   NiceMock<MockMessageHandler> m_messageHandler;
@@ -428,6 +461,10 @@ private:
       TS_ASSERT_EQUALS(presenter.m_batchPresenters[index].get(),
                        m_batchPresenters[index]);
   }
+
+private:
+  std::string backup_facility;
+  std::string backup_instrument;
 };
 
 #endif // MANTID_CUSTOMINTERFACES_MAINWINDOWPRESENTERTEST_H_