diff --git a/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
index b4c892e..419c4ca 100644
--- a/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs.test/META-INF/MANIFEST.MF
@@ -7,7 +7,9 @@
 Bundle-Vendor: %Bundle-Vendor
 Bundle-Localization: plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Import-Package: org.eclipse.jgit.internal.storage.dfs;version="[5.11.0,5.12.0)",
+Import-Package: org.eclipse.jgit.api;version="[5.11.0,5.12.0)",
+ org.eclipse.jgit.attributes;version="[5.11.0,5.12.0)",
+ org.eclipse.jgit.internal.storage.dfs;version="[5.11.0,5.12.0)",
  org.eclipse.jgit.junit;version="[5.11.0,5.12.0)",
  org.eclipse.jgit.lfs;version="[5.11.0,5.12.0)",
  org.eclipse.jgit.lfs.errors;version="[5.11.0,5.12.0)",
diff --git a/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/LfsGitTest.java b/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/LfsGitTest.java
new file mode 100644
index 0000000..8964310
--- /dev/null
+++ b/org.eclipse.jgit.lfs.test/tst/org/eclipse/jgit/lfs/LfsGitTest.java
@@ -0,0 +1,141 @@
+/*
+ * Copyright (C) 2021, Thomas Wolf <thomas.wolf@paranor.ch> and others
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * https://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+package org.eclipse.jgit.lfs;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.ResetCommand.ResetType;
+import org.eclipse.jgit.attributes.FilterCommandRegistry;
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lfs.lib.Constants;
+import org.eclipse.jgit.lib.StoredConfig;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class LfsGitTest extends RepositoryTestCase {
+
+	private static final String SMUDGE_NAME = org.eclipse.jgit.lib.Constants.BUILTIN_FILTER_PREFIX
+			+ Constants.ATTR_FILTER_DRIVER_PREFIX
+			+ org.eclipse.jgit.lib.Constants.ATTR_FILTER_TYPE_SMUDGE;
+
+	private static final String CLEAN_NAME = org.eclipse.jgit.lib.Constants.BUILTIN_FILTER_PREFIX
+			+ Constants.ATTR_FILTER_DRIVER_PREFIX
+			+ org.eclipse.jgit.lib.Constants.ATTR_FILTER_TYPE_CLEAN;
+
+	@BeforeClass
+	public static void installLfs() {
+		FilterCommandRegistry.register(SMUDGE_NAME, SmudgeFilter.FACTORY);
+		FilterCommandRegistry.register(CLEAN_NAME, CleanFilter.FACTORY);
+	}
+
+	@AfterClass
+	public static void removeLfs() {
+		FilterCommandRegistry.unregister(SMUDGE_NAME);
+		FilterCommandRegistry.unregister(CLEAN_NAME);
+	}
+
+	private Git git;
+
+	@Override
+	@Before
+	public void setUp() throws Exception {
+		super.setUp();
+		git = new Git(db);
+		// commit something
+		writeTrashFile("Test.txt", "Hello world");
+		git.add().addFilepattern("Test.txt").call();
+		git.commit().setMessage("Initial commit").call();
+		// prepare the config for LFS
+		StoredConfig config = git.getRepository().getConfig();
+		config.setString("filter", "lfs", "clean", CLEAN_NAME);
+		config.setString("filter", "lfs", "smudge", SMUDGE_NAME);
+		config.save();
+	}
+
+	@Test
+	public void checkoutNonLfsPointer() throws Exception {
+		String content = "size_t\nsome_function(void* ptr);\n";
+		File smallFile = writeTrashFile("Test.txt", content);
+		StringBuilder largeContent = new StringBuilder(
+				LfsPointer.SIZE_THRESHOLD * 4);
+		while (largeContent.length() < LfsPointer.SIZE_THRESHOLD * 4) {
+			largeContent.append(content);
+		}
+		File largeFile = writeTrashFile("large.txt", largeContent.toString());
+		fsTick(largeFile);
+		git.add().addFilepattern("Test.txt").addFilepattern("large.txt").call();
+		git.commit().setMessage("Text files").call();
+		writeTrashFile(".gitattributes", "*.txt filter=lfs");
+		git.add().addFilepattern(".gitattributes").call();
+		git.commit().setMessage("attributes").call();
+		assertTrue(smallFile.delete());
+		assertTrue(largeFile.delete());
+		// This reset will run the two text files through the smudge filter
+		git.reset().setMode(ResetType.HARD).call();
+		assertTrue(smallFile.exists());
+		assertTrue(largeFile.exists());
+		checkFile(smallFile, content);
+		checkFile(largeFile, largeContent.toString());
+		// Modify the large file
+		largeContent.append(content);
+		writeTrashFile("large.txt", largeContent.toString());
+		// This should convert largeFile to an LFS pointer
+		git.add().addFilepattern("large.txt").call();
+		git.commit().setMessage("Large modified").call();
+		String lfsPtr = "version https://git-lfs.github.com/spec/v1\n"
+				+ "oid sha256:d041ab19bd7edd899b3c0450d0f61819f96672f0b22d26c9753abc62e1261614\n"
+				+ "size 858\n";
+		assertEquals("[.gitattributes, mode:100644, content:*.txt filter=lfs]"
+				+ "[Test.txt, mode:100644, content:" + content + ']'
+						+ "[large.txt, mode:100644, content:" + lfsPtr + ']',
+				indexState(CONTENT));
+		// Verify the file has been saved
+		File savedFile = new File(db.getDirectory(), "lfs");
+		savedFile = new File(savedFile, "objects");
+		savedFile = new File(savedFile, "d0");
+		savedFile = new File(savedFile, "41");
+		savedFile = new File(savedFile,
+				"d041ab19bd7edd899b3c0450d0f61819f96672f0b22d26c9753abc62e1261614");
+		String saved = new String(Files.readAllBytes(savedFile.toPath()),
+				StandardCharsets.UTF_8);
+		assertEquals(saved, largeContent.toString());
+
+		assertTrue(smallFile.delete());
+		assertTrue(largeFile.delete());
+		git.reset().setMode(ResetType.HARD).call();
+		assertTrue(smallFile.exists());
+		assertTrue(largeFile.exists());
+		checkFile(smallFile, content);
+		checkFile(largeFile, largeContent.toString());
+		assertEquals("[.gitattributes, mode:100644, content:*.txt filter=lfs]"
+				+ "[Test.txt, mode:100644, content:" + content + ']'
+						+ "[large.txt, mode:100644, content:" + lfsPtr + ']',
+				indexState(CONTENT));
+		git.add().addFilepattern("Test.txt").call();
+		git.commit().setMessage("Small committed again").call();
+		String lfsPtrSmall = "version https://git-lfs.github.com/spec/v1\n"
+				+ "oid sha256:9110463275fb0e2f0e9fdeaf84e598e62915666161145cf08927079119cc7814\n"
+				+ "size 33\n";
+		assertEquals("[.gitattributes, mode:100644, content:*.txt filter=lfs]"
+				+ "[Test.txt, mode:100644, content:" + lfsPtrSmall + ']'
+						+ "[large.txt, mode:100644, content:" + lfsPtr + ']',
+				indexState(CONTENT));
+
+		assertTrue(git.status().call().isClean());
+	}
+}
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsBlobFilter.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsBlobFilter.java
index 52c3001..032a19b 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsBlobFilter.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsBlobFilter.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2017, Markus Duft <markus.duft@ssi-schaefer.com> and others
+ * Copyright (C) 2017, 2021 Markus Duft <markus.duft@ssi-schaefer.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -45,7 +45,7 @@
 	 */
 	public static ObjectLoader smudgeLfsBlob(Repository db, ObjectLoader loader)
 			throws IOException {
-		if (loader.getSize() > LfsPointer.SIZE_THRESHOLD) {
+		if (loader.getSize() > LfsPointer.FULL_SIZE_THRESHOLD) {
 			return loader;
 		}
 
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsPointer.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsPointer.java
index aef4416..0a8a3fa 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsPointer.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsPointer.java
@@ -11,7 +11,9 @@
 
 import static java.nio.charset.StandardCharsets.UTF_8;
 
+import java.io.BufferedInputStream;
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -25,6 +27,7 @@
 import org.eclipse.jgit.lfs.lib.AnyLongObjectId;
 import org.eclipse.jgit.lfs.lib.Constants;
 import org.eclipse.jgit.lfs.lib.LongObjectId;
+import org.eclipse.jgit.util.IO;
 
 /**
  * Represents an LFS pointer file
@@ -57,6 +60,12 @@
 	public static final String HASH_FUNCTION_NAME = Constants.LONG_HASH_FUNCTION
 			.toLowerCase(Locale.ROOT).replace("-", ""); //$NON-NLS-1$ //$NON-NLS-2$
 
+	/**
+	 * {@link #SIZE_THRESHOLD} is too low; with lfs extensions a LFS pointer can
+	 * be larger. But 8kB should be more than enough.
+	 */
+	static final int FULL_SIZE_THRESHOLD = 8 * 1024;
+
 	private final AnyLongObjectId oid;
 
 	private final long size;
@@ -115,64 +124,113 @@
 
 	/**
 	 * Try to parse the data provided by an InputStream to the format defined by
-	 * {@link #VERSION}
+	 * {@link #VERSION}. If the given stream supports mark and reset as
+	 * indicated by {@link InputStream#markSupported()}, its input position will
+	 * be reset if the stream content is not actually a LFS pointer (i.e., when
+	 * {@code null} is returned). If the stream content is an invalid LFS
+	 * pointer or the given stream does not support mark/reset, the input
+	 * position may not be reset.
 	 *
 	 * @param in
 	 *            the {@link java.io.InputStream} from where to read the data
-	 * @return an {@link org.eclipse.jgit.lfs.LfsPointer} or <code>null</code>
-	 *         if the stream was not parseable as LfsPointer
+	 * @return an {@link org.eclipse.jgit.lfs.LfsPointer} or {@code null} if the
+	 *         stream was not parseable as LfsPointer
 	 * @throws java.io.IOException
 	 */
 	@Nullable
 	public static LfsPointer parseLfsPointer(InputStream in)
 			throws IOException {
+		if (in.markSupported()) {
+			return parse(in);
+		}
+		// Fallback; note that while parse() resets its input stream, that won't
+		// reset "in".
+		return parse(new BufferedInputStream(in));
+	}
+
+	@Nullable
+	private static LfsPointer parse(InputStream in)
+			throws IOException {
+		if (!in.markSupported()) {
+			// No translation; internal error
+			throw new IllegalArgumentException(
+					"LFS pointer parsing needs InputStream.markSupported() == true"); //$NON-NLS-1$
+		}
+		// Try reading only a short block first.
+		in.mark(SIZE_THRESHOLD);
+		byte[] preamble = new byte[SIZE_THRESHOLD];
+		int length = IO.readFully(in, preamble, 0);
+		if (length < preamble.length || in.read() < 0) {
+			// We have the whole file. Try to parse a pointer from it.
+			try (BufferedReader r = new BufferedReader(new InputStreamReader(
+					new ByteArrayInputStream(preamble, 0, length), UTF_8))) {
+				LfsPointer ptr = parse(r);
+				if (ptr == null) {
+					in.reset();
+				}
+				return ptr;
+			}
+		}
+		// Longer than SIZE_THRESHOLD: expect "version" to be the first line.
+		boolean hasVersion = checkVersion(preamble);
+		in.reset();
+		if (!hasVersion) {
+			return null;
+		}
+		in.mark(FULL_SIZE_THRESHOLD);
+		byte[] fullPointer = new byte[FULL_SIZE_THRESHOLD];
+		length = IO.readFully(in, fullPointer, 0);
+		if (length == fullPointer.length && in.read() >= 0) {
+			in.reset();
+			return null; // Too long.
+		}
+		try (BufferedReader r = new BufferedReader(new InputStreamReader(
+				new ByteArrayInputStream(fullPointer, 0, length), UTF_8))) {
+			LfsPointer ptr = parse(r);
+			if (ptr == null) {
+				in.reset();
+			}
+			return ptr;
+		}
+	}
+
+	private static LfsPointer parse(BufferedReader r) throws IOException {
 		boolean versionLine = false;
 		LongObjectId id = null;
 		long sz = -1;
-
 		// This parsing is a bit too general if we go by the spec at
 		// https://github.com/git-lfs/git-lfs/blob/master/docs/spec.md
-		// Comment lines are not mentioned in the spec, and the "version" line
-		// MUST be the first.
-		try (BufferedReader br = new BufferedReader(
-				new InputStreamReader(in, UTF_8))) {
-			for (String s = br.readLine(); s != null; s = br.readLine()) {
-				if (s.startsWith("#") || s.length() == 0) { //$NON-NLS-1$
-					continue;
-				} else if (s.startsWith("version")) { //$NON-NLS-1$
-					if (versionLine || s.length() < 8 || s.charAt(7) != ' ') {
-						return null; // Not a LFS pointer
-					}
-					String rest = s.substring(8).trim();
-					versionLine = VERSION.equals(rest)
-							|| VERSION_LEGACY.equals(rest);
-					if (!versionLine) {
-						return null; // Not a LFS pointer
-					}
-				} else {
-					try {
-						if (s.startsWith("oid sha256:")) { //$NON-NLS-1$
-							if (id != null) {
-								return null; // Not a LFS pointer
-							}
-							id = LongObjectId
-									.fromString(s.substring(11).trim());
-						} else if (s.startsWith("size")) { //$NON-NLS-1$
-							if (sz > 0 || s.length() < 5
-									|| s.charAt(4) != ' ') {
-								return null; // Not a LFS pointer
-							}
-							sz = Long.parseLong(s.substring(5).trim());
+		// Comment lines are not mentioned in the spec, the "version" line
+		// MUST be the first, and keys are ordered alphabetically.
+		for (String s = r.readLine(); s != null; s = r.readLine()) {
+			if (s.startsWith("#") || s.length() == 0) { //$NON-NLS-1$
+				continue;
+			} else if (s.startsWith("version")) { //$NON-NLS-1$
+				if (versionLine || !checkVersionLine(s)) {
+					return null; // Not a LFS pointer
+				}
+				versionLine = true;
+			} else {
+				try {
+					if (s.startsWith("oid sha256:")) { //$NON-NLS-1$
+						if (id != null) {
+							return null; // Not a LFS pointer
 						}
-					} catch (RuntimeException e) {
-						// We could not parse the line. If we have a version
-						// already, this is a corrupt LFS pointer. Otherwise it
-						// is just not an LFS pointer.
-						if (versionLine) {
-							throw e;
+						id = LongObjectId.fromString(s.substring(11).trim());
+					} else if (s.startsWith("size")) { //$NON-NLS-1$
+						if (sz > 0 || s.length() < 5 || s.charAt(4) != ' ') {
+							return null; // Not a LFS pointer
 						}
-						return null;
+						sz = Long.parseLong(s.substring(5).trim());
 					}
+				} catch (RuntimeException e) {
+					// We could not parse the line. If we have a version
+					// already, this is a corrupt LFS pointer. Otherwise it
+					// is just not an LFS pointer.
+					if (versionLine) {
+						throw e;
+					}
+					return null;
 				}
 			}
 			if (versionLine && id != null && sz > -1) {
@@ -182,6 +240,30 @@
 		return null;
 	}
 
+	private static boolean checkVersion(byte[] data) {
+		// According to the spec at
+		// https://github.com/git-lfs/git-lfs/blob/master/docs/spec.md
+		// it MUST always be the first line.
+		try (BufferedReader r = new BufferedReader(
+				new InputStreamReader(new ByteArrayInputStream(data), UTF_8))) {
+			String s = r.readLine();
+			if (s != null && s.startsWith("version")) { //$NON-NLS-1$
+				return checkVersionLine(s);
+			}
+		} catch (IOException e) {
+			// Doesn't occur, we're reading from a byte array!
+		}
+		return false;
+	}
+
+	private static boolean checkVersionLine(String s) {
+		if (s.length() < 8 || s.charAt(7) != ' ') {
+			return false; // Not a valid LFS pointer version line
+		}
+		String rest = s.substring(8).trim();
+		return VERSION.equals(rest) || VERSION_LEGACY.equals(rest);
+	}
+
 	/** {@inheritDoc} */
 	@Override
 	public String toString() {
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java
index 2f80d5b..3411887 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/SmudgeFilter.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2016, Christian Halstrick <christian.halstrick@sap.com> and others
+ * Copyright (C) 2016, 2021 Christian Halstrick <christian.halstrick@sap.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -11,6 +11,7 @@
 
 import static java.nio.charset.StandardCharsets.UTF_8;
 
+import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -87,20 +88,31 @@
 	 */
 	public SmudgeFilter(Repository db, InputStream in, OutputStream out)
 			throws IOException {
+		this(in.markSupported() ? in : new BufferedInputStream(in), out, db);
+	}
+
+	private SmudgeFilter(InputStream in, OutputStream out, Repository db)
+			throws IOException {
 		super(in, out);
+		InputStream from = in;
 		try {
-			Lfs lfs = new Lfs(db);
-			LfsPointer res = LfsPointer.parseLfsPointer(in);
+			LfsPointer res = LfsPointer.parseLfsPointer(from);
 			if (res != null) {
 				AnyLongObjectId oid = res.getOid();
+				Lfs lfs = new Lfs(db);
 				Path mediaFile = lfs.getMediaFile(oid);
 				if (!Files.exists(mediaFile)) {
 					downloadLfsResource(lfs, db, res);
 				}
 				this.in = Files.newInputStream(mediaFile);
+			} else {
+				// Not swapped; stream was reset, don't close!
+				from = null;
 			}
 		} finally {
-			in.close(); // make sure the swapped stream is closed properly.
+			if (from != null) {
+				from.close(); // Close the swapped-out stream
+			}
 		}
 	}
 
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/LfsPointerFilter.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/LfsPointerFilter.java
index d84eebd..99bae49 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/LfsPointerFilter.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/LfsPointerFilter.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2015, 2017, Dariusz Luksza <dariusz@luksza.org> and others
+ * Copyright (C) 2015, 2021 Dariusz Luksza <dariusz@luksza.org> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -58,6 +58,8 @@
 		try (ObjectStream stream = object.openStream()) {
 			pointer = LfsPointer.parseLfsPointer(stream);
 			return pointer != null;
+		} catch (RuntimeException e) {
+			return false;
 		}
 	}