diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/InstantComparatorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/InstantComparatorTest.java
new file mode 100644
index 0000000..271b4ea
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/InstantComparatorTest.java
@@ -0,0 +1,182 @@
+/*
+ * Copyright (C) 2019, Thomas Wolf <thomas.wolf@paranor.ch>
+ * 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.treewalk;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.time.Instant;
+
+import org.junit.Test;
+
+public class InstantComparatorTest {
+
+	private final InstantComparator cmp = new InstantComparator();
+
+	@Test
+	public void compareNow() {
+		Instant now = Instant.now();
+		assertEquals(0, cmp.compare(now, now));
+		assertEquals(0, cmp.compare(now, now, true));
+	}
+
+	@Test
+	public void compareSeconds() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond());
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 123456789);
+		assertEquals(0, cmp.compare(t, s));
+		assertEquals(0, cmp.compare(t, t));
+		assertEquals(0, cmp.compare(s, t));
+	}
+
+	@Test
+	public void compareSecondsOnly() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond(), 987654321);
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 123456789);
+		assertEquals(0, cmp.compare(t, s, true));
+		assertEquals(0, cmp.compare(t, t, true));
+		assertEquals(0, cmp.compare(s, t, true));
+	}
+
+	@Test
+	public void compareSecondsUnequal() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond());
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond() - 1L);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+	}
+
+	@Test
+	public void compareMillisEqual() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond(), 123000000);
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 123456789);
+		assertEquals(0, cmp.compare(s, t));
+		assertEquals(0, cmp.compare(t, t));
+		assertEquals(0, cmp.compare(t, s));
+		s = Instant.ofEpochSecond(now.getEpochSecond(), 123456000);
+		assertEquals(0, cmp.compare(s, t));
+		assertEquals(0, cmp.compare(t, s));
+		s = Instant.ofEpochSecond(now.getEpochSecond(), 123400000);
+		assertEquals(0, cmp.compare(s, t));
+		assertEquals(0, cmp.compare(t, s));
+	}
+
+	@Test
+	public void compareMillisUnequal() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond(), 123000000);
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 122000000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		t = Instant.ofEpochSecond(now.getEpochSecond(), 130000000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		t = Instant.ofEpochSecond(now.getEpochSecond(), 200000000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		s = Instant.ofEpochSecond(now.getEpochSecond() - 1L, 123000000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+	}
+
+	@Test
+	public void compareMicrosEqual() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond(), 123456000);
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 123456789);
+		assertEquals(0, cmp.compare(s, t));
+		assertEquals(0, cmp.compare(t, s));
+		s = Instant.ofEpochSecond(now.getEpochSecond(), 123456700);
+		assertEquals(0, cmp.compare(s, t));
+		assertEquals(0, cmp.compare(t, s));
+	}
+
+	@Test
+	public void compareMicrosUnequal() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond(), 123456000);
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 123455000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		t = Instant.ofEpochSecond(now.getEpochSecond(), 123460000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		t = Instant.ofEpochSecond(now.getEpochSecond(), 123500000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		s = Instant.ofEpochSecond(now.getEpochSecond() - 1L, 123456000);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+	}
+
+	@Test
+	public void compareNanosEqual() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond(), 123456789);
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 123456789);
+		assertEquals(0, cmp.compare(s, t));
+		assertEquals(0, cmp.compare(t, s));
+	}
+
+	@Test
+	public void compareNanosUnequal() {
+		Instant now = Instant.now();
+		Instant t = Instant.ofEpochSecond(now.getEpochSecond(), 123456789);
+		Instant s = Instant.ofEpochSecond(now.getEpochSecond(), 123456700);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		t = Instant.ofEpochSecond(now.getEpochSecond(), 123456800);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		s = Instant.ofEpochSecond(now.getEpochSecond() - 1L, 123456789);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+		s = Instant.ofEpochSecond(now.getEpochSecond(), 123456788);
+		assertTrue(cmp.compare(s, t) < 0);
+		assertTrue(cmp.compare(t, s) > 0);
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/InstantComparator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/InstantComparator.java
new file mode 100644
index 0000000..ffcb4b4
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/InstantComparator.java
@@ -0,0 +1,112 @@
+/*
+ * Copyright (C) 2019, Thomas Wolf <thomas.wolf@paranor.ch>
+ * 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.treewalk;
+
+import java.time.Instant;
+import java.util.Comparator;
+
+/**
+ * Specialized comparator for {@link Instant}s. If either timestamp has a zero
+ * fraction, compares only seconds. If either timestamp has no time fraction
+ * smaller than a millisecond, compares only milliseconds. If either timestamp
+ * has no fraction smaller than a microsecond, compares only microseconds.
+ */
+class InstantComparator implements Comparator<Instant> {
+
+	@Override
+	public int compare(Instant a, Instant b) {
+		return compare(a, b, false);
+	}
+
+	/**
+	 * Compares two {@link Instant}s to the lower resolution of the two
+	 * instants. See {@link InstantComparator}.
+	 *
+	 * @param a
+	 *            first {@link Instant} to compare
+	 * @param b
+	 *            second {@link Instant} to compare
+	 * @param forceSecondsOnly
+	 *            whether to omit all fraction comparison
+	 * @return a value &lt; 0 if a &lt; b, a value &gt; 0 if a &gt; b, and 0 if
+	 *         a == b
+	 */
+	public int compare(Instant a, Instant b, boolean forceSecondsOnly) {
+		long aSeconds = a.getEpochSecond();
+		long bSeconds = b.getEpochSecond();
+		int result = Long.compare(aSeconds, bSeconds);
+		if (result != 0) {
+			return result;
+		}
+		int aSubSecond = a.getNano();
+		int bSubSecond = b.getNano();
+		if (forceSecondsOnly || (aSubSecond == 0)
+				|| (bSubSecond == 0)) {
+			// Don't check the subseconds part.
+			return 0;
+		} else if (aSubSecond != bSubSecond) {
+			// If either has nothing smaller than a millisecond, compare only
+			// milliseconds.
+			int aSubMillis = aSubSecond % 1_000_000;
+			int bSubMillis = bSubSecond % 1_000_000;
+			if (aSubMillis == 0) {
+				bSubSecond -= bSubMillis;
+			} else if (bSubMillis == 0) {
+				aSubSecond -= aSubMillis;
+			} else {
+				// Same again, but for microsecond resolution. NTFS has 100ns
+				// resolution, but WindowsFileAttributes may provide only
+				// microseconds (1000ns). Similar for some Unix file systems.
+				int aSubMicros = aSubSecond % 1000;
+				int bSubMicros = bSubSecond % 1000;
+				if (aSubMicros == 0) {
+					bSubSecond -= bSubMicros;
+				} else if (bSubMicros == 0) {
+					aSubSecond -= aSubMicros;
+				}
+			}
+		}
+		return Integer.compare(aSubSecond, bSubSecond);
+	}
+
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
index 53fa3bc..e8ff1a9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
@@ -175,6 +175,9 @@
 	/** The offset of the content id in {@link #idBuffer()} */
 	private int contentIdOffset;
 
+	/** A comparator for {@link Instant}s. */
+	private final InstantComparator timestampComparator = new InstantComparator();
+
 	/**
 	 * Create a new iterator with no parent.
 	 *
@@ -936,27 +939,19 @@
 		if (!entry.isSmudged() && entry.getLength() != (int) getEntryLength())
 			return MetadataDiff.DIFFER_BY_METADATA;
 
-		// Git under windows only stores seconds so we round the timestamp
-		// Java gives us if it looks like the timestamp in index is seconds
-		// only. Otherwise we compare the timestamp at nanosecond precision,
-		// unless core.checkstat is set to "minimal", in which case we only
-		// compare the whole second part.
+		// Cache and file timestamps may differ in resolution. Therefore don't
+		// compare instants directly but use a comparator that compares only
+		// up to the lower apparent resolution of either timestamp.
+		//
+		// If core.checkstat is set to "minimal", compare only the seconds part.
 		Instant cacheLastModified = entry.getLastModifiedInstant();
 		Instant fileLastModified = getEntryLastModifiedInstant();
-		if ((getOptions().getCheckStat() == CheckStat.MINIMAL)
-				|| (cacheLastModified.getNano() == 0)
-				// Some Java version on Linux return whole seconds only even
-				// when the file systems supports more precision.
-				|| (fileLastModified.getNano() == 0)) {
-			if (fileLastModified.getEpochSecond() != cacheLastModified
-					.getEpochSecond()) {
-				return MetadataDiff.DIFFER_BY_TIMESTAMP;
-			} else if (entry.isSmudged()) {
-				return MetadataDiff.SMUDGED;
-			}
-		} else if (!fileLastModified.equals(cacheLastModified)) {
+		if (timestampComparator.compare(cacheLastModified, fileLastModified,
+				getOptions().getCheckStat() == CheckStat.MINIMAL) != 0) {
 			return MetadataDiff.DIFFER_BY_TIMESTAMP;
-		} else if (entry.isSmudged()) {
+		}
+
+		if (entry.isSmudged()) {
 			return MetadataDiff.SMUDGED;
 		}
 		// The file is clean when when comparing timestamps