diff --git a/codeflash/cli_cmds/github_workflow.py b/codeflash/cli_cmds/github_workflow.py
index 4f9431657..c295d66a0 100644
--- a/codeflash/cli_cmds/github_workflow.py
+++ b/codeflash/cli_cmds/github_workflow.py
@@ -37,6 +37,7 @@ class DependencyManager(Enum):
 def install_github_actions(override_formatter_check: bool = False, *, skip_confirm: bool = False) -> None:
     try:
         config, _config_file_path = parse_config_file(override_formatter_check=override_formatter_check)
+        interactive_stdin = sys.stdin.isatty()
 
         ph("cli-github-actions-install-started")
         try:
@@ -102,6 +103,8 @@ def install_github_actions(override_formatter_check: bool = False, *, skip_confi
 
             if skip_confirm:
                 benchmark_mode = True
+            elif not interactive_stdin:
+                benchmark_mode = False
             else:
                 benchmark_questions = [
                     inquirer.Confirm("benchmark_mode", message="Run GitHub Actions in benchmark mode?", default=True)
@@ -126,6 +129,8 @@ def install_github_actions(override_formatter_check: bool = False, *, skip_confi
 
         if skip_confirm:
             confirm_creation = True
+        elif not interactive_stdin:
+            confirm_creation = False
         else:
             creation_questions = [
                 inquirer.Confirm(
diff --git a/codeflash/cli_cmds/init_config.py b/codeflash/cli_cmds/init_config.py
index f1cb053d6..bd72453a6 100644
--- a/codeflash/cli_cmds/init_config.py
+++ b/codeflash/cli_cmds/init_config.py
@@ -80,6 +80,18 @@ def get_toml_key(self) -> str:
 }
 
 
+def confirm_with_default_on_eof(
+    prompt: str, *, default: bool, show_default: bool = True, **kwargs: Any
+) -> bool:
+    """Return the prompt default instead of crashing when stdin is unavailable."""
+    from rich.prompt import Confirm
+
+    try:
+        return Confirm.ask(prompt, default=default, show_default=show_default, **kwargs)
+    except EOFError:
+        return default
+
+
 @lru_cache(maxsize=1)
 def get_valid_subdirs(current_dir: Optional[Path] = None) -> list[str]:
 
@@ -148,8 +160,6 @@ def should_modify_pyproject_toml(*, skip_confirm: bool = False) -> tuple[bool, d
 
     If it does, ask the user if they want to re-configure it.
     """
-    from rich.prompt import Confirm
-
     pyproject_toml_path = Path.cwd() / "pyproject.toml"
 
     found, _ = config_found(pyproject_toml_path)
@@ -164,7 +174,7 @@ def should_modify_pyproject_toml(*, skip_confirm: bool = False) -> tuple[bool, d
     if skip_confirm:
         return False, config
 
-    return Confirm.ask(
+    return confirm_with_default_on_eof(
         "✅ A valid Codeflash config already exists in this project. Do you want to re-configure it?",
         default=False,
         show_default=True,
@@ -285,9 +295,7 @@ def create_empty_pyproject_toml(pyproject_toml_path: Path) -> None:
 
 def ask_for_telemetry() -> bool:
     """Prompt the user to enable or disable telemetry."""
-    from rich.prompt import Confirm
-
-    return Confirm.ask(
+    return confirm_with_default_on_eof(
         "⚡️ Help us improve Codeflash by sharing anonymous usage data (e.g. errors encountered)?",
         default=True,
         show_default=True,
diff --git a/codeflash/cli_cmds/init_java.py b/codeflash/cli_cmds/init_java.py
index 4d110751e..8475e5edc 100644
--- a/codeflash/cli_cmds/init_java.py
+++ b/codeflash/cli_cmds/init_java.py
@@ -20,6 +20,7 @@
 from rich.text import Text
 
 from codeflash.cli_cmds.console import apologize_and_exit, console
+from codeflash.cli_cmds.init_config import confirm_with_default_on_eof
 from codeflash.code_utils.code_utils import validate_relative_directory_path
 from codeflash.code_utils.compat import LF
 from codeflash.code_utils.git_utils import get_git_remotes
@@ -215,8 +216,6 @@ def init_java_project(*, skip_confirm: bool = False, skip_api_key: bool = False)
 
 def should_modify_java_config(*, skip_confirm: bool = False) -> tuple[bool, dict[str, Any] | None]:
     """Check if the project already has Codeflash config."""
-    from rich.prompt import Confirm
-
     project_root = Path.cwd()
 
     # Check for existing codeflash config in pom.xml properties or gradle.properties
@@ -228,7 +227,7 @@ def should_modify_java_config(*, skip_confirm: bool = False) -> tuple[bool, dict
         if existing:
             if skip_confirm:
                 return False, None
-            return Confirm.ask(
+            return confirm_with_default_on_eof(
                 "A Codeflash config already exists. Do you want to re-configure it?", default=False, show_default=True
             ), None
     except ValueError:
@@ -239,8 +238,6 @@ def should_modify_java_config(*, skip_confirm: bool = False) -> tuple[bool, dict
 
 def collect_java_setup_info(*, skip_confirm: bool = False) -> JavaSetupInfo:
     """Collect setup information for Java projects."""
-    from rich.prompt import Confirm
-
     from codeflash.cli_cmds.init_config import ask_for_telemetry
 
     curdir = Path.cwd()
@@ -282,7 +279,7 @@ def collect_java_setup_info(*, skip_confirm: bool = False) -> JavaSetupInfo:
     test_root_override = None
     formatter_override = None
 
-    if Confirm.ask("Would you like to change any of these settings?", default=False):
+    if confirm_with_default_on_eof("Would you like to change any of these settings?", default=False):
         # Source root override
         module_root_override = _prompt_directory_override("source", detected_source_root, curdir)
 
diff --git a/codeflash/cli_cmds/init_javascript.py b/codeflash/cli_cmds/init_javascript.py
index 6e7f407f3..23b19dea6 100644
--- a/codeflash/cli_cmds/init_javascript.py
+++ b/codeflash/cli_cmds/init_javascript.py
@@ -19,7 +19,6 @@
 from git import InvalidGitRepositoryError, Repo
 from rich.console import Group
 from rich.panel import Panel
-from rich.prompt import Confirm
 from rich.table import Table
 from rich.text import Text
 
@@ -297,6 +296,8 @@ def init_js_project(language: ProjectLanguage, *, skip_confirm: bool = False, sk
 
 def should_modify_package_json_config(*, skip_confirm: bool = False) -> tuple[bool, dict[str, Any] | None]:
     """Check if package.json has valid codeflash config for JS/TS projects."""
+    from codeflash.cli_cmds.init_config import confirm_with_default_on_eof
+
     package_json_path = Path("package.json")
 
     if not package_json_path.exists():
@@ -326,7 +327,7 @@ def should_modify_package_json_config(*, skip_confirm: bool = False) -> tuple[bo
             return False, config
 
         # Config is valid - ask if user wants to reconfigure
-        return Confirm.ask(
+        return confirm_with_default_on_eof(
             "✅ A valid Codeflash config already exists in package.json. Do you want to re-configure it?",
             default=False,
             show_default=True,
@@ -341,7 +342,7 @@ def collect_js_setup_info(language: ProjectLanguage, *, skip_confirm: bool = Fal
     Uses auto-detection for most settings and only asks for overrides if needed.
     When skip_confirm is True, uses all auto-detected defaults without prompting.
     """
-    from codeflash.cli_cmds.init_config import ask_for_telemetry, get_valid_subdirs
+    from codeflash.cli_cmds.init_config import ask_for_telemetry, confirm_with_default_on_eof, get_valid_subdirs
     from codeflash.code_utils.config_js import (
         detect_formatter,
         detect_module_root,
@@ -378,8 +379,6 @@ def collect_js_setup_info(language: ProjectLanguage, *, skip_confirm: bool = Fal
             pass
         return JSSetupInfo(git_remote=git_remote)
 
-    from rich.prompt import Confirm
-
     # Build detection summary
     formatter_display = detected_formatter[0] if detected_formatter else "none detected"
     detection_table = Table(show_header=False, box=None, padding=(0, 2))
@@ -401,7 +400,7 @@ def collect_js_setup_info(language: ProjectLanguage, *, skip_confirm: bool = Fal
     module_root_override = None
     formatter_override = None
 
-    if Confirm.ask("Would you like to change any of these settings?", default=False):
+    if confirm_with_default_on_eof("Would you like to change any of these settings?", default=False):
         # Module root override
         valid_subdirs = get_valid_subdirs()
         curdir_option = f"current directory ({curdir})"
diff --git a/tests/test_github_workflow.py b/tests/test_github_workflow.py
index 083f463e0..06ed4896e 100644
--- a/tests/test_github_workflow.py
+++ b/tests/test_github_workflow.py
@@ -53,3 +53,27 @@ def test_install_github_actions_skip_confirm_supports_go_projects(tmp_path: Path
     assert "Optimize new Go code" in workflow_text
     assert "actions/setup-go@v5" in workflow_text
     assert "go mod download" in workflow_text
+
+
+def test_install_github_actions_non_tty_skips_optional_setup(tmp_path: Path, monkeypatch) -> None:
+    monkeypatch.chdir(tmp_path)
+    Repo.init(tmp_path)
+    (tmp_path / "tests").mkdir()
+    (tmp_path / "pyproject.toml").write_text(
+        """
+[tool.codeflash]
+module-root = "."
+tests-root = "tests"
+formatter-cmds = ["disabled"]
+""".strip(),
+        encoding="utf-8",
+    )
+
+    stdin = type("Stdin", (), {"isatty": lambda self: False})()
+    monkeypatch.setattr("codeflash.cli_cmds.github_workflow.sys.stdin", stdin)
+
+    with patch("codeflash.cli_cmds.github_workflow.inquirer.prompt") as mock_prompt:
+        install_github_actions()
+
+    mock_prompt.assert_not_called()
+    assert not (tmp_path / ".github" / "workflows" / "codeflash.yaml").exists()
diff --git a/tests/test_init_java_go.py b/tests/test_init_java_go.py
index 0fa08168c..1edc44090 100644
--- a/tests/test_init_java_go.py
+++ b/tests/test_init_java_go.py
@@ -27,6 +27,21 @@ def test_collect_go_setup_info_skip_confirm_uses_defaults(tmp_path: Path, monkey
     assert setup_info.disable_telemetry is False
 
 
+def test_collect_go_setup_info_uses_default_telemetry_on_eof(tmp_path: Path, monkeypatch) -> None:
+    monkeypatch.chdir(tmp_path)
+    (tmp_path / "go.mod").write_text("module example.com/demo\n\ngo 1.21\n", encoding="utf-8")
+
+    get_git_remote = Mock(return_value="origin")
+    monkeypatch.setattr("codeflash.cli_cmds.init_go._get_git_remote_for_setup", get_git_remote)
+
+    with patch("rich.prompt.Confirm.ask", side_effect=EOFError):
+        setup_info = collect_go_setup_info()
+
+    get_git_remote.assert_called_once_with()
+    assert setup_info.git_remote == "origin"
+    assert setup_info.disable_telemetry is False
+
+
 def test_collect_java_setup_info_skip_confirm_uses_defaults(tmp_path: Path, monkeypatch) -> None:
     monkeypatch.chdir(tmp_path)
     (tmp_path / "build.gradle").write_text("plugins { id 'java' }\n", encoding="utf-8")
@@ -52,6 +67,30 @@ def test_collect_java_setup_info_skip_confirm_uses_defaults(tmp_path: Path, monk
     assert setup_info.disable_telemetry is False
 
 
+def test_collect_java_setup_info_uses_defaults_on_eof(tmp_path: Path, monkeypatch) -> None:
+    monkeypatch.chdir(tmp_path)
+    (tmp_path / "build.gradle").write_text("plugins { id 'java' }\n", encoding="utf-8")
+    (tmp_path / "src" / "main" / "java").mkdir(parents=True)
+    (tmp_path / "src" / "test" / "java").mkdir(parents=True)
+
+    get_git_remote = Mock(return_value="origin")
+    monkeypatch.setattr("codeflash.cli_cmds.init_java._get_git_remote_for_setup", get_git_remote)
+    monkeypatch.setattr("codeflash.cli_cmds.init_config.ask_for_telemetry", Mock(return_value=True))
+
+    with patch("codeflash.cli_cmds.init_java.inquirer") as mock_inquirer, patch(
+        "rich.prompt.Confirm.ask", side_effect=EOFError
+    ):
+        setup_info = collect_java_setup_info()
+
+    mock_inquirer.prompt.assert_not_called()
+    get_git_remote.assert_called_once_with()
+    assert setup_info.module_root_override is None
+    assert setup_info.test_root_override is None
+    assert setup_info.formatter_override is None
+    assert setup_info.git_remote == "origin"
+    assert setup_info.disable_telemetry is False
+
+
 def test_should_modify_java_config_skip_confirm_skips_reconfigure_prompt(tmp_path: Path, monkeypatch) -> None:
     monkeypatch.chdir(tmp_path)
     (tmp_path / "build.gradle").write_text("plugins { id 'java' }\n", encoding="utf-8")
@@ -62,3 +101,15 @@ def test_should_modify_java_config_skip_confirm_skips_reconfigure_prompt(tmp_pat
 
     assert should_modify is False
     assert config is None
+
+
+def test_should_modify_java_config_uses_default_on_eof(tmp_path: Path, monkeypatch) -> None:
+    monkeypatch.chdir(tmp_path)
+    (tmp_path / "build.gradle").write_text("plugins { id 'java' }\n", encoding="utf-8")
+    (tmp_path / "gradle.properties").write_text("codeflash.moduleRoot=src/main/java\n", encoding="utf-8")
+
+    with patch("rich.prompt.Confirm.ask", side_effect=EOFError):
+        should_modify, config = should_modify_java_config()
+
+    assert should_modify is False
+    assert config is None
diff --git a/tests/test_init_javascript.py b/tests/test_init_javascript.py
index acc959579..8c93e8959 100644
--- a/tests/test_init_javascript.py
+++ b/tests/test_init_javascript.py
@@ -3,13 +3,14 @@
 import json
 import tempfile
 from pathlib import Path
-from unittest.mock import patch
+from unittest.mock import Mock, patch
 
 import pytest
 
 from codeflash.cli_cmds.init_javascript import (
     JsPackageManager,
     ProjectLanguage,
+    collect_js_setup_info,
     detect_project_language,
     determine_js_package_manager,
     get_package_install_command,
@@ -334,6 +335,20 @@ def test_should_modify_skip_confirm_with_invalid_config(
         assert should_modify is True
         assert config is None
 
+    def test_should_modify_valid_config_uses_default_on_eof(
+        self, tmp_project: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        """EOF on the reconfigure prompt should keep the existing config."""
+        monkeypatch.chdir(tmp_project)
+        codeflash_config = {"moduleRoot": "."}
+        (tmp_project / "package.json").write_text(json.dumps({"name": "test", "codeflash": codeflash_config}))
+
+        with patch("rich.prompt.Confirm.ask", side_effect=EOFError):
+            should_modify, config = should_modify_package_json_config()
+
+        assert should_modify is False
+        assert config == codeflash_config
+
 
 class TestCollectJsSetupInfoSkipConfirm:
     """Tests for collect_js_setup_info with skip_confirm."""
@@ -354,6 +369,30 @@ def test_collect_js_setup_info_skip_confirm(self, tmp_project: Path, monkeypatch
         assert setup_info.formatter_override is None
         assert setup_info.git_remote == "origin"
 
+    def test_collect_js_setup_info_uses_defaults_on_eof(
+        self, tmp_project: Path, monkeypatch: pytest.MonkeyPatch
+    ) -> None:
+        """EOF on the settings confirm should keep auto-detected defaults."""
+        monkeypatch.chdir(tmp_project)
+        (tmp_project / "package.json").write_text(json.dumps({"name": "test"}))
+
+        get_git_remote = Mock(return_value="origin")
+        monkeypatch.setattr("codeflash.cli_cmds.init_javascript._get_git_remote_for_setup", get_git_remote)
+        monkeypatch.setattr("codeflash.cli_cmds.init_config.ask_for_telemetry", Mock(return_value=True))
+
+        with (
+            patch("rich.prompt.Confirm.ask", side_effect=EOFError),
+            patch("codeflash.cli_cmds.init_javascript.inquirer") as mock_inquirer,
+        ):
+            setup_info = collect_js_setup_info(ProjectLanguage.JAVASCRIPT)
+
+        mock_inquirer.prompt.assert_not_called()
+        get_git_remote.assert_called_once_with()
+        assert setup_info.module_root_override is None
+        assert setup_info.formatter_override is None
+        assert setup_info.git_remote == "origin"
+        assert setup_info.disable_telemetry is False
+
 
 class TestDetectProjectLanguage:
     """Tests for detect_project_language function."""
diff --git a/tests/test_init_yes.py b/tests/test_init_yes.py
index 2ed287526..393ec7df1 100644
--- a/tests/test_init_yes.py
+++ b/tests/test_init_yes.py
@@ -66,6 +66,23 @@ def test_should_modify_pyproject_toml_skip_confirm_skips_reconfigure_prompt(
     assert config["git_remote"] == "upstream"
 
 
+def test_should_modify_pyproject_toml_uses_default_on_eof(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
+    monkeypatch.chdir(tmp_path)
+    (tmp_path / "src").mkdir()
+    (tmp_path / "tests").mkdir()
+    (tmp_path / "pyproject.toml").write_text(
+        '[tool.codeflash]\nmodule-root = "src"\ntests-root = "tests"\ngit-remote = "upstream"\n',
+        encoding="utf-8",
+    )
+
+    with patch("rich.prompt.Confirm.ask", side_effect=EOFError):
+        should_modify, config = should_modify_pyproject_toml()
+
+    assert should_modify is False
+    assert config is not None
+    assert config["git_remote"] == "upstream"
+
+
 def test_init_codeflash_skip_confirm_reuses_existing_python_config(
     tmp_path: Path, monkeypatch: pytest.MonkeyPatch
 ) -> None: