diff --git a/pygmt/session_management.py b/pygmt/session_management.py
index cafd306e120..e814daf4fb8 100644
--- a/pygmt/session_management.py
+++ b/pygmt/session_management.py
@@ -15,6 +15,8 @@ def begin():
     prefix = "pygmt-session"
     with Session() as lib:
         lib.call_module("begin", prefix)
+        # pygmt relies on GMT modern mode with GMT_COMPATIBILITY at version 6
+        lib.call_module("set", "GMT_COMPATIBILITY 6")
 
 
 def end():
diff --git a/pygmt/tests/test_session_management.py b/pygmt/tests/test_session_management.py
index e69f24ec49b..6ca9afa75b5 100644
--- a/pygmt/tests/test_session_management.py
+++ b/pygmt/tests/test_session_management.py
@@ -20,3 +20,33 @@ def test_begin_end():
     begin()  # Restart the global session
     assert os.path.exists("pygmt-session.pdf")
     os.remove("pygmt-session.pdf")
+
+
+def test_gmt_compat_6_is_applied(capsys):
+    """
+    Ensure that users with old gmt.conf files won't get pygmt-session [ERROR]:
+    GMT_COMPATIBILITY: Expects values from 6 to 6; reset to 6.
+    """
+    end()  # Kill the global session
+    try:
+        with Session() as lib:
+            # pretend that gmt.conf has GMT_COMPATIBILITY = 5
+            lib.call_module("gmtset", "GMT_COMPATIBILITY 5")
+        begin()
+        with Session() as lib:
+            lib.call_module("basemap", "-R10/70/-3/8 -JX4i/3i -Ba")
+            out, err = capsys.readouterr()  # capture stdout and stderr
+            assert out == ""
+            assert err != (
+                "pygmt-session [ERROR]: GMT_COMPATIBILITY:"
+                " Expects values from 6 to 6; reset to 6.\n"
+            )
+            assert err == ""  # double check that there are no other errors
+    finally:
+        with Session() as lib:
+            # revert gmt.conf back to GMT_COMPATIBILITY = 6
+            lib.call_module("set", "GMT_COMPATIBILITY 6")
+        end()
+        begin()  # Restart the global session
+        assert os.path.exists("pygmt-session.pdf")
+        os.remove("pygmt-session.pdf")