diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/SystemReaderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/SystemReaderTest.java
new file mode 100644
index 0000000..1fe1ba9
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/SystemReaderTest.java
@@ -0,0 +1,127 @@
+/*
+ * Copyright (C) 2019, Matthias Sohn <matthias.sohn@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.when;
+
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Mock;
+import org.mockito.junit.MockitoJUnitRunner;
+
+@RunWith(MockitoJUnitRunner.class)
+public class SystemReaderTest {
+	private Path trash;
+
+	private Path mockSystemConfig;
+
+	private Path mockUserConfig;
+
+	@Mock
+	private FS fs;
+
+	@Before
+	public void setup() throws Exception {
+		trash = Files.createTempDirectory("jgit_test");
+		mockSystemConfig = trash.resolve("systemgitconfig");
+		Files.write(mockSystemConfig, "[core]\n  trustFolderStat = false\n"
+				.getBytes(StandardCharsets.UTF_8));
+		mockUserConfig = trash.resolve(".gitconfig");
+		Files.write(mockUserConfig,
+				"[core]\n  bare = false\n".getBytes(StandardCharsets.UTF_8));
+		when(fs.getGitSystemConfig()).thenReturn(mockSystemConfig.toFile());
+		when(fs.userHome()).thenReturn(trash.toFile());
+		SystemReader.setInstance(null);
+	}
+
+	@After
+	public void teardown() throws Exception {
+		FileUtils.delete(trash.toFile(), FileUtils.RECURSIVE | FileUtils.RETRY);
+	}
+
+	@Test
+	public void openSystemConfigReturnsDifferentInstances() throws Exception {
+		FileBasedConfig system1 = SystemReader.getInstance()
+				.openSystemConfig(null, fs);
+		system1.load();
+		assertEquals("false",
+				system1.getString("core", null, "trustFolderStat"));
+
+		FileBasedConfig system2 = SystemReader.getInstance()
+				.openSystemConfig(null, fs);
+		system2.load();
+		assertEquals("false",
+				system2.getString("core", null, "trustFolderStat"));
+
+		system1.setString("core", null, "trustFolderStat", "true");
+		assertEquals("true",
+				system1.getString("core", null, "trustFolderStat"));
+		assertEquals("false",
+				system2.getString("core", null, "trustFolderStat"));
+	}
+
+	@Test
+	public void openUserConfigReturnsDifferentInstances() throws Exception {
+		FileBasedConfig user1 = SystemReader.getInstance().openUserConfig(null,
+				fs);
+		user1.load();
+		assertEquals("false", user1.getString("core", null, "bare"));
+
+		FileBasedConfig user2 = SystemReader.getInstance().openUserConfig(null,
+				fs);
+		user2.load();
+		assertEquals("false", user2.getString("core", null, "bare"));
+
+		user1.setString("core", null, "bare", "true");
+		assertEquals("true", user1.getString("core", null, "bare"));
+		assertEquals("false", user2.getString("core", null, "bare"));
+	}
+}
diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index cfc6866..cbb9de1 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -233,18 +233,6 @@
         </filter>
     </resource>
     <resource path="src/org/eclipse/jgit/util/SystemReader.java" type="org.eclipse.jgit.util.SystemReader">
-        <filter id="336695337">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.util.SystemReader"/>
-                <message_argument value="getSystemConfig()"/>
-            </message_arguments>
-        </filter>
-        <filter id="336695337">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.util.SystemReader"/>
-                <message_argument value="getUserConfig()"/>
-            </message_arguments>
-        </filter>
         <filter id="1142947843">
             <message_arguments>
                 <message_argument value="5.1.9"/>
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
index 310bc83..cccac66 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java
@@ -98,10 +98,6 @@
 	private static class Default extends SystemReader {
 		private volatile String hostname;
 
-		private AtomicReference<FileBasedConfig> systemConfig = new AtomicReference<>();
-
-		private volatile AtomicReference<FileBasedConfig> userConfig = new AtomicReference<>();
-
 		@Override
 		public String getenv(String variable) {
 			return System.getenv(variable);
@@ -114,23 +110,14 @@
 
 		@Override
 		public FileBasedConfig openSystemConfig(Config parent, FS fs) {
-			FileBasedConfig c = systemConfig.get();
-			if (c == null) {
-				systemConfig.compareAndSet(null,
-						createSystemConfig(parent, fs));
-				c = systemConfig.get();
-			}
-			return c;
-		}
-
-		protected FileBasedConfig createSystemConfig(Config parent, FS fs) {
-			if (StringUtils.isEmptyOrNull(getenv(Constants.GIT_CONFIG_NOSYSTEM_KEY))) {
+			if (StringUtils
+					.isEmptyOrNull(getenv(Constants.GIT_CONFIG_NOSYSTEM_KEY))) {
 				File configFile = fs.getGitSystemConfig();
 				if (configFile != null) {
 					return new FileBasedConfig(parent, configFile, fs);
 				}
 			}
-			return new FileBasedConfig(null, fs) {
+			return new FileBasedConfig(parent, null, fs) {
 				@Override
 				public void load() {
 					// empty, do not load
@@ -146,35 +133,8 @@
 
 		@Override
 		public FileBasedConfig openUserConfig(Config parent, FS fs) {
-			FileBasedConfig c = userConfig.get();
-			if (c == null) {
-				userConfig.compareAndSet(null, new FileBasedConfig(parent,
-						new File(fs.userHome(), ".gitconfig"), fs)); //$NON-NLS-1$
-				c = userConfig.get();
-			}
-			return c;
-		}
-
-		@Override
-		public StoredConfig getSystemConfig()
-				throws IOException, ConfigInvalidException {
-			FileBasedConfig c = openSystemConfig(null, FS.DETECTED);
-			if (c.isOutdated()) {
-				LOG.debug("loading system config {}", systemConfig); //$NON-NLS-1$
-				c.load();
-			}
-			return c;
-		}
-
-		@Override
-		public StoredConfig getUserConfig()
-				throws IOException, ConfigInvalidException {
-			FileBasedConfig c = openUserConfig(getSystemConfig(), FS.DETECTED);
-			if (c.isOutdated()) {
-				LOG.debug("loading user config {}", userConfig); //$NON-NLS-1$
-				c.load();
-			}
-			return c;
+			return new FileBasedConfig(parent, new File(fs.userHome(), ".gitconfig"), //$NON-NLS-1$
+					fs);
 		}
 
 		@Override
@@ -234,6 +194,10 @@
 
 	private ObjectChecker platformChecker;
 
+	private AtomicReference<FileBasedConfig> systemConfig = new AtomicReference<>();
+
+	private AtomicReference<FileBasedConfig> userConfig = new AtomicReference<>();
+
 	private void init() {
 		// Creating ObjectChecker must be deferred. Unit tests change
 		// behavior of is{Windows,MacOS} in constructor of subclass.
@@ -323,8 +287,23 @@
 	 *             if something went wrong when reading files
 	 * @since 5.1.9
 	 */
-	public abstract StoredConfig getUserConfig()
-			throws IOException, ConfigInvalidException;
+	public StoredConfig getUserConfig()
+			throws IOException, ConfigInvalidException {
+		FileBasedConfig c = userConfig.get();
+		if (c == null) {
+			userConfig.compareAndSet(null,
+					openUserConfig(getSystemConfig(), FS.DETECTED));
+			c = userConfig.get();
+		} else {
+			// Ensure the parent is up to date
+			getSystemConfig();
+		}
+		if (c.isOutdated()) {
+			LOG.debug("loading user config {}", userConfig); //$NON-NLS-1$
+			c.load();
+		}
+		return c;
+	}
 
 	/**
 	 * Get the gitconfig configuration found in the system-wide "etc" directory.
@@ -339,8 +318,20 @@
 	 *             if something went wrong when reading files
 	 * @since 5.1.9
 	 */
-	public abstract StoredConfig getSystemConfig()
-			throws IOException, ConfigInvalidException;
+	public StoredConfig getSystemConfig()
+			throws IOException, ConfigInvalidException {
+		FileBasedConfig c = systemConfig.get();
+		if (c == null) {
+			systemConfig.compareAndSet(null,
+					openSystemConfig(null, FS.DETECTED));
+			c = systemConfig.get();
+		}
+		if (c.isOutdated()) {
+			LOG.debug("loading system config {}", systemConfig); //$NON-NLS-1$
+			c.load();
+		}
+		return c;
+	}
 
 	/**
 	 * Get the current system time