diff --git a/pylsp/_utils.py b/pylsp/_utils.py
index 9ac30cfc..0732067a 100644
--- a/pylsp/_utils.py
+++ b/pylsp/_utils.py
@@ -6,12 +6,17 @@
 import logging
 import os
 import pathlib
+import re
 import threading
 
 import jedi
 
 JEDI_VERSION = jedi.__version__
 
+# Eol chars accepted by the LSP protocol
+EOL_CHARS = ['\r\n', '\r', '\n']
+EOL_REGEX = re.compile(f'({"|".join(EOL_CHARS)})')
+
 log = logging.getLogger(__name__)
 
 
@@ -220,3 +225,11 @@ def is_process_alive(pid):
             return e.errno == errno.EPERM
         else:
             return True
+
+
+def get_eol_chars(text):
+    """Get EOL chars used in text."""
+    match = EOL_REGEX.search(text)
+    if match:
+        return match.group(0)
+    return None
diff --git a/pylsp/plugins/autopep8_format.py b/pylsp/plugins/autopep8_format.py
index f62443f6..8915fb72 100644
--- a/pylsp/plugins/autopep8_format.py
+++ b/pylsp/plugins/autopep8_format.py
@@ -2,9 +2,12 @@
 # Copyright 2021- Python Language Server Contributors.
 
 import logging
+
 import pycodestyle
 from autopep8 import fix_code, continued_indentation as autopep8_c_i
+
 from pylsp import hookimpl
+from pylsp._utils import get_eol_chars
 
 log = logging.getLogger(__name__)
 
@@ -38,15 +41,27 @@ def _format(config, document, line_range=None):
     del pycodestyle._checks['logical_line'][pycodestyle.continued_indentation]
     pycodestyle.register_check(autopep8_c_i)
 
-    new_source = fix_code(document.source, options=options)
+    # Autopep8 doesn't work with CR line endings, so we replace them by '\n'
+    # and restore them below.
+    replace_cr = False
+    source = document.source
+    eol_chars = get_eol_chars(source)
+    if eol_chars == '\r':
+        replace_cr = True
+        source = source.replace('\r', '\n')
+
+    new_source = fix_code(source, options=options)
 
     # Switch it back
     del pycodestyle._checks['logical_line'][autopep8_c_i]
     pycodestyle.register_check(pycodestyle.continued_indentation)
 
-    if new_source == document.source:
+    if new_source == source:
         return []
 
+    if replace_cr:
+        new_source = new_source.replace('\n', '\r')
+
     # I'm too lazy at the moment to parse diffs into TextEdit items
     # So let's just return the entire file...
     return [{
diff --git a/pylsp/plugins/yapf_format.py b/pylsp/plugins/yapf_format.py
index 6728007b..1c90f965 100644
--- a/pylsp/plugins/yapf_format.py
+++ b/pylsp/plugins/yapf_format.py
@@ -3,9 +3,12 @@
 
 import logging
 import os
+
 from yapf.yapflib import file_resources
 from yapf.yapflib.yapf_api import FormatCode
+
 from pylsp import hookimpl
+from pylsp._utils import get_eol_chars
 
 log = logging.getLogger(__name__)
 
@@ -34,8 +37,17 @@ def pylsp_format_range(document, range):  # pylint: disable=redefined-builtin
 
 
 def _format(document, lines=None):
+    # Yapf doesn't work with CR line endings, so we replace them by '\n'
+    # and restore them below.
+    replace_cr = False
+    source = document.source
+    eol_chars = get_eol_chars(source)
+    if eol_chars == '\r':
+        replace_cr = True
+        source = source.replace('\r', '\n')
+
     new_source, changed = FormatCode(
-        document.source,
+        source,
         lines=lines,
         filename=document.filename,
         style_config=file_resources.GetDefaultStyleForDir(
@@ -46,6 +58,9 @@ def _format(document, lines=None):
     if not changed:
         return []
 
+    if replace_cr:
+        new_source = new_source.replace('\n', '\r')
+
     # I'm too lazy at the moment to parse diffs into TextEdit items
     # So let's just return the entire file...
     return [{
diff --git a/test/plugins/test_autopep8_format.py b/test/plugins/test_autopep8_format.py
index cfb7bb60..1e790aaa 100644
--- a/test/plugins/test_autopep8_format.py
+++ b/test/plugins/test_autopep8_format.py
@@ -71,3 +71,10 @@ def test_hanging_indentation(config, workspace):
 
     assert len(res) == 1
     assert res[0]['newText'] == CORRECT_INDENTED_DOC
+
+
+def test_cr_line_endings(config, workspace):
+    doc = Document(DOC_URI, workspace, 'import os;import sys\r\rdict(a=1)')
+    res = pylsp_format_document(config, doc)
+
+    assert res[0]['newText'] == 'import os\rimport sys\r\rdict(a=1)\r'
diff --git a/test/plugins/test_yapf_format.py b/test/plugins/test_yapf_format.py
index 90410432..4346985c 100644
--- a/test/plugins/test_yapf_format.py
+++ b/test/plugins/test_yapf_format.py
@@ -58,3 +58,10 @@ def test_config_file(tmpdir, workspace):
 
     # A was split on multiple lines because of column_limit from config file
     assert pylsp_format_document(doc)[0]['newText'] == "A = [\n    'h', 'w',\n    'a'\n]\n\nB = ['h', 'w']\n"
+
+
+def test_cr_line_endings(workspace):
+    doc = Document(DOC_URI, workspace, 'import os;import sys\r\rdict(a=1)')
+    res = pylsp_format_document(doc)
+
+    assert res[0]['newText'] == 'import os\rimport sys\r\rdict(a=1)\r'