diff --git a/test/test_environment.py b/test/test_environment.py
index f37133aac..d9dd6a312 100644
--- a/test/test_environment.py
+++ b/test/test_environment.py
@@ -8,6 +8,7 @@
 from asv import config, environment, util
 from asv.repo import get_repo
 from asv.util import shlex_quote as quote
+from . import tools
 
 from .tools import (PYTHON_VER1, PYTHON_VER2, DUMMY1_VERSION, DUMMY2_VERSIONS, WIN, HAS_PYPY,
                     HAS_CONDA, HAS_VIRTUALENV, HAS_PYTHON_VER2, generate_test_repo)
@@ -682,6 +683,7 @@ def test_build_isolation(tmpdir):
     env.install_project(conf, repo, commit_hash)
 
 
+@pytest.mark.skipif(tools.HAS_PYPY, reason="Flaky on pypy")
 def test_custom_commands(tmpdir):
     # check custom install/uninstall/build commands work
     tmpdir = str(tmpdir)
diff --git a/test/test_publish.py b/test/test_publish.py
index 095158e41..9ee43659b 100644
--- a/test/test_publish.py
+++ b/test/test_publish.py
@@ -442,6 +442,7 @@ def test_regression_atom_feed_update(dvcs_type, tmpdir):
         b_content = b.find('{http://www.w3.org/2005/Atom}content')
         assert a_content.text != b_content.text
 
+@pytest.mark.skipif(tools.HAS_PYPY, reason="Flaky on pypy")
 def test_branch_name_is_also_filename(tmpdir):
     # gh-1209
     tmpdir = str(tmpdir)