diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index c818dd7187..dc6daa1456 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -1571,6 +1571,7 @@ def test_extension_fake_modules(self):
         eb.builddir = config.build_path()
         eb.installdir = config.install_path()
 
+        update_build_option('trace', True)
         self.mock_stdout(True)
         eb.extensions_step(fetch=True)
         stdout = self.get_stdout()
diff --git a/test/framework/filetools.py b/test/framework/filetools.py
index dc781c1c7c..8eb5f452cf 100644
--- a/test/framework/filetools.py
+++ b/test/framework/filetools.py
@@ -2508,6 +2508,7 @@ def test_extract_file(self):
         build_options = {
             'extended_dry_run': True,
             'silent': False,
+            'trace': True
         }
         init_config(build_options=build_options)
 
@@ -3071,6 +3072,7 @@ def test_github_get_source_tarball_from_git(self):
         build_options = {
             'extended_dry_run': True,
             'silent': False,
+            'trace': True,
         }
         init_config(build_options=build_options)
 
diff --git a/test/framework/run.py b/test/framework/run.py
index c7c4e0e66b..827d76b431 100644
--- a/test/framework/run.py
+++ b/test/framework/run.py
@@ -541,9 +541,6 @@ def test_run_shell_cmd_fail(self):
         def handler(signum, _):
             raise RuntimeError("Signal handler called with signal %s" % signum)
 
-        # disable trace output for this test (so stdout remains empty)
-        update_build_option('trace', False)
-
         orig_sigalrm_handler = signal.getsignal(signal.SIGALRM)
 
         try:
@@ -811,6 +808,8 @@ def test_run_shell_cmd_split_stderr(self):
     def test_run_cmd_trace(self):
         """Test run_cmd in trace mode, and with tracing disabled."""
 
+        update_build_option('trace', True)
+
         # use of run_cmd is deprecated, so we need to allow it here
         self.allow_deprecated_behaviour()
 
@@ -837,8 +836,7 @@ def test_run_cmd_trace(self):
         regex = re.compile('\n'.join(pattern))
         self.assertTrue(regex.search(stdout), "Pattern '%s' found in: %s" % (regex.pattern, stdout))
 
-        init_config(build_options={'trace': False})
-
+        update_build_option('trace', False)
         self.mock_stdout(True)
         self.mock_stderr(True)
         (out, ec) = run_cmd("echo hello")
@@ -851,9 +849,8 @@ def test_run_cmd_trace(self):
         self.assertTrue(stderr.strip().startswith("WARNING: Deprecated functionality"))
         self.assertEqual(stdout, '')
 
-        init_config(build_options={'trace': True})
-
         # also test with command that is fed input via stdin
+        update_build_option('trace', True)
         self.mock_stdout(True)
         self.mock_stderr(True)
         (out, ec) = run_cmd('cat', inp='hello')
@@ -869,8 +866,7 @@ def test_run_cmd_trace(self):
         regex = re.compile('\n'.join(pattern))
         self.assertTrue(regex.search(stdout), "Pattern '%s' found in: %s" % (regex.pattern, stdout))
 
-        init_config(build_options={'trace': False})
-
+        update_build_option('trace', False)
         self.mock_stdout(True)
         self.mock_stderr(True)
         (out, ec) = run_cmd('cat', inp='hello')
@@ -902,6 +898,8 @@ def test_run_cmd_trace(self):
     def test_run_shell_cmd_trace(self):
         """Test run_shell_cmd function in trace mode, and with tracing disabled."""
 
+        update_build_option('trace', True)
+
         pattern = [
             r"^  >> running shell command:",
             r"\techo hello",
@@ -911,7 +909,6 @@ def test_run_shell_cmd_trace(self):
             r"  >> command completed: exit 0, ran in .*",
         ]
 
-        # trace output is enabled by default (since EasyBuild v5.0)
         self.mock_stdout(True)
         self.mock_stderr(True)
         res = run_shell_cmd("echo hello")
@@ -926,7 +923,6 @@ def test_run_shell_cmd_trace(self):
         self.assertTrue(regex.search(stdout), "Pattern '%s' found in: %s" % (regex.pattern, stdout))
 
         init_config(build_options={'trace': False})
-
         self.mock_stdout(True)
         self.mock_stderr(True)
         res = run_shell_cmd("echo hello")
@@ -939,8 +935,6 @@ def test_run_shell_cmd_trace(self):
         self.assertEqual(stderr, '')
         self.assertEqual(stdout, '')
 
-        init_config(build_options={'trace': True})
-
         # trace output can be disabled on a per-command basis via 'hidden' option
         for trace in (True, False):
             init_config(build_options={'trace': trace})
@@ -1297,6 +1291,7 @@ def test_run_shell_cmd_qa_log(self):
 
     def test_run_cmd_qa_trace(self):
         """Test run_cmd under --trace"""
+        update_build_option('trace', True)
 
         # use of run_cmd/run_cmd_qa is deprecated, so we need to allow it here
         self.allow_deprecated_behaviour()
@@ -1331,8 +1326,8 @@ def test_run_cmd_qa_trace(self):
 
     def test_run_shell_cmd_qa_trace(self):
         """Test run_shell_cmd with qa_patterns under --trace"""
+        update_build_option('trace', True)
 
-        # --trace is enabled by default
         self.mock_stdout(True)
         self.mock_stderr(True)
         run_shell_cmd("echo 'n: '; read n; seq 1 $n", qa_patterns=[('n: ', '5')])
@@ -1572,6 +1567,7 @@ def test_run_shell_cmd_dry_run(self):
         build_options = {
             'extended_dry_run': True,
             'silent': False,
+            'trace': True,
         }
         init_config(build_options=build_options)
 
@@ -1718,6 +1714,7 @@ def test_run_cmd_stream(self):
 
     def test_run_shell_cmd_stream(self):
         """Test use of run_shell_cmd with streaming output."""
+        init_config(build_options={'trace': True})
         self.mock_stdout(True)
         self.mock_stderr(True)
         cmd = '; '.join([
@@ -2059,9 +2056,6 @@ def post_run_shell_cmd_hook(cmd, *args, **kwargs):
         write_file(hooks_file, hooks_file_txt)
         update_build_option('hooks', hooks_file)
 
-        # disable trace output to make checking of generated output produced by hooks easier
-        update_build_option('trace', False)
-
         with self.mocked_stdout_stderr():
             run_cmd("make")
             stdout = self.get_stdout()
@@ -2133,9 +2127,6 @@ def post_run_shell_cmd_hook(cmd, *args, **kwargs):
         write_file(hooks_file, hooks_file_txt)
         update_build_option('hooks', hooks_file)
 
-        # disable trace output to make checking of generated output produced by hooks easier
-        update_build_option('trace', False)
-
         with self.mocked_stdout_stderr():
             run_shell_cmd("make")
             stdout = self.get_stdout()
diff --git a/test/framework/toolchain.py b/test/framework/toolchain.py
index 11f5b5b0e3..7217b1bb14 100644
--- a/test/framework/toolchain.py
+++ b/test/framework/toolchain.py
@@ -2023,8 +2023,7 @@ def test_old_new_iccifort(self):
         scalapack_mt_shared_libs_fosscuda = scalapack_mt_static_libs_fosscuda.replace('.a', '.' + shlib_ext)
 
         tc = self.get_toolchain('fosscuda', version='2018a')
-        with self.mocked_stdout_stderr():
-            tc.prepare()
+        tc.prepare()
         self.assertEqual(os.environ['BLAS_SHARED_LIBS'], blas_shared_libs_fosscuda)
         self.assertEqual(os.environ['BLAS_STATIC_LIBS'], blas_static_libs_fosscuda)
         self.assertEqual(os.environ['BLAS_MT_SHARED_LIBS'], blas_mt_shared_libs_fosscuda)
@@ -2116,8 +2115,7 @@ def test_old_new_iccifort(self):
         self.modtool.purge()
 
         tc = self.get_toolchain('intel', version='2018a')
-        with self.mocked_stdout_stderr():
-            tc.prepare()
+        tc.prepare()
         self.assertEqual(os.environ.get('BLAS_SHARED_LIBS', "(not set)"), blas_shared_libs_intel4)
         self.assertEqual(os.environ.get('BLAS_STATIC_LIBS', "(not set)"), blas_static_libs_intel4)
         self.assertEqual(os.environ.get('LAPACK_SHARED_LIBS', "(not set)"), blas_shared_libs_intel4)
@@ -2130,22 +2128,19 @@ def test_old_new_iccifort(self):
         self.modtool.purge()
 
         tc = self.get_toolchain('intel', version='2012a')
-        with self.mocked_stdout_stderr():
-            tc.prepare()
+        tc.prepare()
         self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_intel3)
         self.assertIn(libscalack_intel3, os.environ['LIBSCALAPACK'])
         self.modtool.purge()
 
         tc = self.get_toolchain('intel', version='2018a')
-        with self.mocked_stdout_stderr():
-            tc.prepare()
+        tc.prepare()
         self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_intel4)
         self.assertIn(libscalack_intel4, os.environ['LIBSCALAPACK'])
         self.modtool.purge()
 
         tc = self.get_toolchain('intel', version='2012a')
-        with self.mocked_stdout_stderr():
-            tc.prepare()
+        tc.prepare()
         self.assertEqual(os.environ.get('LIBBLAS_MT', "(not set)"), libblas_mt_intel3)
         self.assertIn(libscalack_intel3, os.environ['LIBSCALAPACK'])
         self.modtool.purge()
@@ -2154,15 +2149,13 @@ def test_old_new_iccifort(self):
         tc = self.get_toolchain('intel', version='2018a')
         opts = {'i8': True}
         tc.set_options(opts)
-        with self.mocked_stdout_stderr():
-            tc.prepare()
+        tc.prepare()
         self.assertIn(libscalack_intel4, os.environ['LIBSCALAPACK'])
         self.modtool.purge()
 
         tc = self.get_toolchain('fosscuda', version='2018a')
         tc.set_options({'openmp': True})
-        with self.mocked_stdout_stderr():
-            tc.prepare()
+        tc.prepare()
         self.assertEqual(os.environ['BLAS_SHARED_LIBS'], blas_shared_libs_fosscuda)
         self.assertEqual(os.environ['BLAS_STATIC_LIBS'], blas_static_libs_fosscuda)
         self.assertEqual(os.environ['BLAS_MT_SHARED_LIBS'], blas_mt_shared_libs_fosscuda)
diff --git a/test/framework/toy_build.py b/test/framework/toy_build.py
index 9e110ba09b..973f76ac03 100644
--- a/test/framework/toy_build.py
+++ b/test/framework/toy_build.py
@@ -52,7 +52,7 @@
 from easybuild.framework.easyconfig.parser import EasyConfigParser
 from easybuild.main import main_with_hooks
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import get_module_syntax, get_repositorypath
+from easybuild.tools.config import get_module_syntax, get_repositorypath, update_build_option
 from easybuild.tools.environment import setvar
 from easybuild.tools.filetools import adjust_permissions, change_dir, copy_file, mkdir, move_file
 from easybuild.tools.filetools import read_file, remove_dir, remove_file, which, write_file
@@ -159,7 +159,7 @@ def check_toy(self, installpath, outtxt, name='toy', version='0.0', versionprefi
 
     def _test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True, fails=False, verbose=True,
                         raise_error=False, test_report=None, name='toy', versionsuffix='', testing=True,
-                        raise_systemexit=False, force=True, test_report_regexs=None, debug=True):
+                        raise_systemexit=False, force=True, test_report_regexs=None, debug=True, trace=True):
         """Perform a toy build."""
         if extra_args is None:
             extra_args = []
@@ -175,6 +175,8 @@ def _test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=Tru
         ]
         if debug:
             args.append('--debug')
+        if trace:
+            args.append('--trace')
         if force:
             args.append('--force')
         if tmpdir is not None:
@@ -3142,6 +3144,7 @@ def test_toy_filter_rpath_sanity_libs(self):
 
     def test_toy_cuda_sanity_check(self):
         """Test the CUDA sanity check"""
+        update_build_option('trace', True)
         # Define the toy_ec file we want to use
         topdir = os.path.dirname(os.path.abspath(__file__))
         toy_ec = os.path.join(topdir, 'easyconfigs', 'test_ecs', 't', 'toy', 'toy-0.0.eb')
diff --git a/test/framework/utilities.py b/test/framework/utilities.py
index 16a441f655..d17ef2da29 100644
--- a/test/framework/utilities.py
+++ b/test/framework/utilities.py
@@ -137,6 +137,8 @@ def setUp(self):
         # disable progress bars when running the tests,
         # since it messes with test suite progress output when test installations are performed
         os.environ['EASYBUILD_DISABLE_SHOW_PROGRESS_BAR'] = '1'
+        # Also disable trace output to keep stdout clean during tests
+        os.environ['EASYBUILD_DISABLE_TRACE'] = '1'
 
         # Store the environment as setup (including the above paths) for tests to restore
         self.orig_environ = copy.deepcopy(os.environ)
@@ -487,25 +489,24 @@ def init_config(args=None, build_options=None, with_include=True, clear_caches=T
     eb_go = eboptions.parse_options(args=args, with_include=with_include)
     config.init(eb_go.options, eb_go.get_options_by_section('config'))
 
-    # initialize build options
-    if build_options is None:
-        build_options = {}
-
-    default_build_options = {
+    # initialize default build options
+    options = {
         'extended_dry_run': False,
         'external_modules_metadata': ConfigObj(),
         'local_var_naming_check': 'error',
+        'show_progress_bar': False,
         'silence_deprecation_warnings': eb_go.options.silence_deprecation_warnings,
         'suffix_modules_path': GENERAL_CLASS,
+        'trace': False,
         'unit_testing_mode': True,
         'valid_module_classes': module_classes(),
         'valid_stops': [x[0] for x in EasyBlock.get_steps()],
     }
-    for key, def_option in default_build_options.items():
-        if key not in build_options:
-            build_options[key] = def_option
 
-    config.init_build_options(build_options=build_options)
+    if build_options is not None:
+        options.update(build_options)
+
+    config.init_build_options(build_options=options)
 
     return eb_go.options