diff --git a/pygmt/tests/test_x2sys_cross.py b/pygmt/tests/test_x2sys_cross.py
index 5d3ced83aa2..2665def26ed 100644
--- a/pygmt/tests/test_x2sys_cross.py
+++ b/pygmt/tests/test_x2sys_cross.py
@@ -3,6 +3,7 @@
 Tests for x2sys_cross
 """
 import os
+import shutil
 from tempfile import TemporaryDirectory
 
 import numpy as np
@@ -19,10 +20,14 @@
 @pytest.fixture(name="mock_x2sys_home")
 def fixture_mock_x2sys_home(monkeypatch):
     """
-    Set the X2SYS_HOME environment variable to the current working directory
-    for the test session
+    Set the X2SYS_HOME environment variable to "X2SYS_TMP" in the current
+    working directory for the test session
     """
-    monkeypatch.setenv("X2SYS_HOME", os.getcwd())
+    x2sys_home = os.path.join(os.getcwd(), "X2SYS_TMP")
+    os.makedirs(name=x2sys_home, exist_ok=True)
+    monkeypatch.setenv("X2SYS_HOME", x2sys_home)
+    yield x2sys_home
+    shutil.rmtree(x2sys_home)  # cleanup X2SYS_TMP directory after tests
 
 
 @pytest.fixture(scope="module", name="tracks")
@@ -39,7 +44,7 @@ def test_x2sys_cross_input_file_output_file(mock_x2sys_home):
     Run x2sys_cross by passing in a filename, and output internal crossovers to
     an ASCII txt file
     """
-    with TemporaryDirectory(prefix="X2SYS", dir=os.getcwd()) as tmpdir:
+    with TemporaryDirectory(prefix="X2SYS", dir=mock_x2sys_home) as tmpdir:
         tag = os.path.basename(tmpdir)
         x2sys_init(tag=tag, fmtfile="xyz", force=True)
         outfile = os.path.join(tmpdir, "tmp_coe.txt")
@@ -59,7 +64,7 @@ def test_x2sys_cross_input_file_output_dataframe(mock_x2sys_home):
     Run x2sys_cross by passing in a filename, and output internal crossovers to
     a pandas.DataFrame
     """
-    with TemporaryDirectory(prefix="X2SYS", dir=os.getcwd()) as tmpdir:
+    with TemporaryDirectory(prefix="X2SYS", dir=mock_x2sys_home) as tmpdir:
         tag = os.path.basename(tmpdir)
         x2sys_init(tag=tag, fmtfile="xyz", force=True)
         output = x2sys_cross(tracks=["@tut_ship.xyz"], tag=tag, coe="i", verbose="i")
@@ -79,7 +84,7 @@ def test_x2sys_cross_input_dataframe_output_dataframe(mock_x2sys_home, tracks):
     to a pandas.DataFrame. Not actually implemented yet, wait for
     https://github.com/GenericMappingTools/gmt/issues/3717
     """
-    with TemporaryDirectory(prefix="X2SYS", dir=os.getcwd()) as tmpdir:
+    with TemporaryDirectory(prefix="X2SYS", dir=mock_x2sys_home) as tmpdir:
         tag = os.path.basename(tmpdir)
         x2sys_init(tag=tag, fmtfile="xyz", force=True)
 
@@ -102,7 +107,7 @@ def test_x2sys_cross_input_two_filenames(mock_x2sys_home):
     Run x2sys_cross by passing in two filenames, and output external crossovers
     to a pandas.DataFrame
     """
-    with TemporaryDirectory(prefix="X2SYS", dir=os.getcwd()) as tmpdir:
+    with TemporaryDirectory(prefix="X2SYS", dir=mock_x2sys_home) as tmpdir:
         tag = os.path.basename(tmpdir)
         x2sys_init(tag=tag, fmtfile="xyz", force=True)
 
@@ -142,7 +147,7 @@ def test_x2sys_cross_region_interpolation_numpoints(mock_x2sys_home):
     Test that x2sys_cross's region (R), interpolation (l) and numpoints (W)
     arguments work.
     """
-    with TemporaryDirectory(prefix="X2SYS", dir=os.getcwd()) as tmpdir:
+    with TemporaryDirectory(prefix="X2SYS", dir=mock_x2sys_home) as tmpdir:
         tag = os.path.basename(tmpdir)
         x2sys_init(tag=tag, fmtfile="xyz", force=True)
         output = x2sys_cross(
@@ -165,7 +170,7 @@ def test_x2sys_cross_trackvalues(mock_x2sys_home):
     """
     Test that x2sys_cross's trackvalues (Z) argument work.
     """
-    with TemporaryDirectory(prefix="X2SYS", dir=os.getcwd()) as tmpdir:
+    with TemporaryDirectory(prefix="X2SYS", dir=mock_x2sys_home) as tmpdir:
         tag = os.path.basename(tmpdir)
         x2sys_init(tag=tag, fmtfile="xyz", force=True)
         output = x2sys_cross(tracks=["@tut_ship.xyz"], tag=tag, trackvalues=True)