diff --git a/scripts/bash/check-prerequisites.sh b/scripts/bash/check-prerequisites.sh
index 88a5559460..b244ea7a5b 100644
--- a/scripts/bash/check-prerequisites.sh
+++ b/scripts/bash/check-prerequisites.sh
@@ -78,13 +78,12 @@ done
 SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
-# Get feature paths and validate branch
+# Get feature paths
 _paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
 eval "$_paths_output"
 unset _paths_output
-check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 
-# If paths-only mode, output paths and exit (support JSON + paths-only combined)
+# If paths-only mode, output paths and exit (no validation)
 if $PATHS_ONLY; then
     if $JSON_MODE; then
         # Minimal JSON paths payload (no validation performed)
@@ -112,6 +111,9 @@ if $PATHS_ONLY; then
     exit 0
 fi
 
+# Validate branch name
+check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
+
 # Validate required directories and files
 if [[ ! -d "$FEATURE_DIR" ]]; then
     echo "ERROR: Feature directory not found: $FEATURE_DIR" >&2
diff --git a/scripts/bash/setup-plan.sh b/scripts/bash/setup-plan.sh
index f2d2f6e6fc..945385c643 100644
--- a/scripts/bash/setup-plan.sh
+++ b/scripts/bash/setup-plan.sh
@@ -40,15 +40,31 @@ fi
 # Ensure the feature directory exists
 mkdir -p "$FEATURE_DIR"
 
-# Copy plan template if it exists
-TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
-if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
-    cp "$TEMPLATE" "$IMPL_PLAN"
-    echo "Copied plan template to $IMPL_PLAN"
+# Copy plan template if plan doesn't already exist
+if [[ -f "$IMPL_PLAN" ]]; then
+    if $JSON_MODE; then
+        echo "Plan already exists at $IMPL_PLAN, skipping template copy" >&2
+    else
+        echo "Plan already exists at $IMPL_PLAN, skipping template copy"
+    fi
 else
-    echo "Warning: Plan template not found"
-    # Create a basic plan file if template doesn't exist
-    touch "$IMPL_PLAN"
+    TEMPLATE=$(resolve_template "plan-template" "$REPO_ROOT") || true
+    if [[ -n "$TEMPLATE" ]] && [[ -f "$TEMPLATE" ]]; then
+        cp "$TEMPLATE" "$IMPL_PLAN"
+        if $JSON_MODE; then
+            echo "Copied plan template to $IMPL_PLAN" >&2
+        else
+            echo "Copied plan template to $IMPL_PLAN"
+        fi
+    else
+        if $JSON_MODE; then
+            echo "Warning: Plan template not found" >&2
+        else
+            echo "Warning: Plan template not found"
+        fi
+        # Create a basic plan file if template doesn't exist
+        touch "$IMPL_PLAN"
+    fi
 fi
 
 # Output results
diff --git a/scripts/powershell/check-prerequisites.ps1 b/scripts/powershell/check-prerequisites.ps1
index 91667e9ef1..0620fa0e70 100644
--- a/scripts/powershell/check-prerequisites.ps1
+++ b/scripts/powershell/check-prerequisites.ps1
@@ -56,14 +56,10 @@ EXAMPLES:
 # Source common functions
 . "$PSScriptRoot/common.ps1"
 
-# Get feature paths and validate branch
+# Get feature paths
 $paths = Get-FeaturePathsEnv
 
-if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit:$paths.HAS_GIT)) { 
-    exit 1 
-}
-
-# If paths-only mode, output paths and exit (support combined -Json -PathsOnly)
+# If paths-only mode, output paths and exit (no validation)
 if ($PathsOnly) {
     if ($Json) {
         [PSCustomObject]@{
@@ -85,6 +81,11 @@ if ($PathsOnly) {
     exit 0
 }
 
+# Validate branch name
+if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit:$paths.HAS_GIT)) {
+    exit 1
+}
+
 # Validate required directories and files
 if (-not (Test-Path $paths.FEATURE_DIR -PathType Container)) {
     Write-Output "ERROR: Feature directory not found: $($paths.FEATURE_DIR)"
diff --git a/scripts/powershell/setup-plan.ps1 b/scripts/powershell/setup-plan.ps1
index cd9cf8c426..d9eecdf75c 100644
--- a/scripts/powershell/setup-plan.ps1
+++ b/scripts/powershell/setup-plan.ps1
@@ -33,17 +33,25 @@ if (-not (Test-FeatureJsonMatchesFeatureDir -RepoRoot $paths.REPO_ROOT -ActiveFe
 # Ensure the feature directory exists
 New-Item -ItemType Directory -Path $paths.FEATURE_DIR -Force | Out-Null
 
-# Copy plan template if it exists, otherwise note it or create empty file
-$template = Resolve-Template -TemplateName 'plan-template' -RepoRoot $paths.REPO_ROOT
-if ($template -and (Test-Path $template)) { 
-    # Read the template content and write it to the implementation plan file with UTF-8 encoding without BOM
-    $content = [System.IO.File]::ReadAllText($template)
-    $utf8NoBom = New-Object System.Text.UTF8Encoding($false)
-    [System.IO.File]::WriteAllText($paths.IMPL_PLAN, $content, $utf8NoBom)
+# Copy plan template if plan doesn't already exist
+if (Test-Path $paths.IMPL_PLAN -PathType Leaf) {
+    if ($Json) {
+        [Console]::Error.WriteLine("Plan already exists at $($paths.IMPL_PLAN), skipping template copy")
+    } else {
+        Write-Output "Plan already exists at $($paths.IMPL_PLAN), skipping template copy"
+    }
 } else {
-    Write-Warning "Plan template not found"
-    # Create a basic plan file if template doesn't exist
-    New-Item -ItemType File -Path $paths.IMPL_PLAN -Force | Out-Null
+    $template = Resolve-Template -TemplateName 'plan-template' -RepoRoot $paths.REPO_ROOT
+    if ($template -and (Test-Path $template)) {
+        # Read the template content and write it to the implementation plan file with UTF-8 encoding without BOM
+        $content = [System.IO.File]::ReadAllText($template)
+        $utf8NoBom = New-Object System.Text.UTF8Encoding($false)
+        [System.IO.File]::WriteAllText($paths.IMPL_PLAN, $content, $utf8NoBom)
+    } else {
+        Write-Warning "Plan template not found"
+        # Create a basic plan file if template doesn't exist
+        New-Item -ItemType File -Path $paths.IMPL_PLAN -Force | Out-Null
+    }
 }
 
 # Output results
diff --git a/tests/test_check_prerequisites_paths_only.py b/tests/test_check_prerequisites_paths_only.py
new file mode 100644
index 0000000000..2e03028001
--- /dev/null
+++ b/tests/test_check_prerequisites_paths_only.py
@@ -0,0 +1,205 @@
+"""Tests for check-prerequisites --paths-only skipping branch validation (#2653)."""
+
+import json
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+
+from tests.conftest import requires_bash
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
+CHECK_PREREQS_SH = PROJECT_ROOT / "scripts" / "bash" / "check-prerequisites.sh"
+COMMON_PS = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+CHECK_PREREQS_PS = PROJECT_ROOT / "scripts" / "powershell" / "check-prerequisites.ps1"
+
+HAS_PWSH = shutil.which("pwsh") is not None
+_POWERSHELL = shutil.which("powershell.exe") or shutil.which("powershell")
+
+
+def _install_bash_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "bash"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_SH, d / "common.sh")
+    shutil.copy(CHECK_PREREQS_SH, d / "check-prerequisites.sh")
+
+
+def _install_ps_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "powershell"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_PS, d / "common.ps1")
+    shutil.copy(CHECK_PREREQS_PS, d / "check-prerequisites.ps1")
+
+
+def _clean_env() -> dict[str, str]:
+    env = os.environ.copy()
+    for key in list(env):
+        if key.startswith("SPECIFY_"):
+            env.pop(key)
+    return env
+
+
+def _git_init(repo: Path) -> None:
+    subprocess.run(["git", "init", "-q"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@example.com"], cwd=repo, check=True
+    )
+    subprocess.run(["git", "config", "user.name", "Test User"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=repo, check=True
+    )
+
+
+@pytest.fixture
+def prereq_repo(tmp_path: Path) -> Path:
+    repo = tmp_path / "proj"
+    repo.mkdir()
+    _git_init(repo)
+    (repo / ".specify").mkdir()
+    _install_bash_scripts(repo)
+    _install_ps_scripts(repo)
+    return repo
+
+
+# ── Bash tests ────────────────────────────────────────────────────────────
+
+
+@requires_bash
+def test_paths_only_succeeds_on_non_spec_branch(prereq_repo: Path) -> None:
+    """--paths-only must return paths without branch validation (main branch)."""
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json", "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "REPO_ROOT" in data
+    assert "BRANCH" in data
+    assert "FEATURE_DIR" in data
+
+
+@requires_bash
+def test_paths_only_succeeds_on_spec_branch(prereq_repo: Path) -> None:
+    """--paths-only must also work on a properly named spec branch."""
+    subprocess.run(
+        ["git", "checkout", "-q", "-b", "001-my-feature"],
+        cwd=prereq_repo,
+        check=True,
+    )
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json", "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "FEATURE_DIR" in data
+    assert "001-my-feature" in data.get("BRANCH", "")
+
+
+@requires_bash
+def test_paths_only_text_mode_on_non_spec_branch(prereq_repo: Path) -> None:
+    """--paths-only without --json must return text paths on a non-spec branch."""
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    assert "REPO_ROOT:" in result.stdout
+    assert "FEATURE_DIR:" in result.stdout
+
+
+@requires_bash
+def test_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
+    """Without --paths-only, branch validation must still fail on main."""
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode != 0
+    assert "Not on a feature branch" in result.stderr
+
+
+# ── PowerShell tests ──────────────────────────────────────────────────────
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_paths_only_succeeds_on_non_spec_branch(prereq_repo: Path) -> None:
+    """-PathsOnly must return paths without branch validation (main branch)."""
+    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json", "-PathsOnly"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "REPO_ROOT" in data
+    assert "BRANCH" in data
+    assert "FEATURE_DIR" in data
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_paths_only_succeeds_on_spec_branch(prereq_repo: Path) -> None:
+    """-PathsOnly must also work on a properly named spec branch."""
+    subprocess.run(
+        ["git", "checkout", "-q", "-b", "001-my-feature"],
+        cwd=prereq_repo,
+        check=True,
+    )
+    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json", "-PathsOnly"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "FEATURE_DIR" in data
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
+    """Without -PathsOnly, branch validation must still fail on main."""
+    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode != 0
+    assert "Not on a feature branch" in result.stderr
diff --git a/tests/test_setup_plan_no_overwrite.py b/tests/test_setup_plan_no_overwrite.py
new file mode 100644
index 0000000000..f29a629294
--- /dev/null
+++ b/tests/test_setup_plan_no_overwrite.py
@@ -0,0 +1,216 @@
+"""Tests for setup-plan preserving existing plan.md (#2653)."""
+
+import json
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+
+from tests.conftest import requires_bash
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
+SETUP_PLAN_SH = PROJECT_ROOT / "scripts" / "bash" / "setup-plan.sh"
+COMMON_PS = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+SETUP_PLAN_PS = PROJECT_ROOT / "scripts" / "powershell" / "setup-plan.ps1"
+PLAN_TEMPLATE = PROJECT_ROOT / "templates" / "plan-template.md"
+
+HAS_PWSH = shutil.which("pwsh") is not None
+_POWERSHELL = shutil.which("powershell.exe") or shutil.which("powershell")
+
+
+def _install_bash_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "bash"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_SH, d / "common.sh")
+    shutil.copy(SETUP_PLAN_SH, d / "setup-plan.sh")
+
+
+def _install_ps_scripts(repo: Path) -> None:
+    d = repo / ".specify" / "scripts" / "powershell"
+    d.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_PS, d / "common.ps1")
+    shutil.copy(SETUP_PLAN_PS, d / "setup-plan.ps1")
+
+
+def _minimal_templates(repo: Path) -> None:
+    tdir = repo / ".specify" / "templates"
+    tdir.mkdir(parents=True, exist_ok=True)
+    shutil.copy(PLAN_TEMPLATE, tdir / "plan-template.md")
+
+
+def _clean_env() -> dict[str, str]:
+    env = os.environ.copy()
+    for key in list(env):
+        if key.startswith("SPECIFY_"):
+            env.pop(key)
+    return env
+
+
+def _git_init(repo: Path) -> None:
+    subprocess.run(["git", "init", "-q"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@example.com"], cwd=repo, check=True
+    )
+    subprocess.run(["git", "config", "user.name", "Test User"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=repo, check=True
+    )
+
+
+@pytest.fixture
+def plan_repo(tmp_path: Path) -> Path:
+    repo = tmp_path / "proj"
+    repo.mkdir()
+    _git_init(repo)
+    subprocess.run(
+        ["git", "checkout", "-q", "-b", "001-my-feature"],
+        cwd=repo,
+        check=True,
+    )
+    (repo / ".specify").mkdir()
+    _minimal_templates(repo)
+    _install_bash_scripts(repo)
+    _install_ps_scripts(repo)
+    return repo
+
+
+# ── Bash tests ────────────────────────────────────────────────────────────
+
+
+@requires_bash
+def test_setup_plan_creates_plan_when_missing(plan_repo: Path) -> None:
+    """First run must create plan.md from the template."""
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    plan_path = Path(data["IMPL_PLAN"])
+    assert plan_path.is_file()
+    # Template content should be present
+    content = plan_path.read_text(encoding="utf-8")
+    assert len(content) > 0
+
+
+@requires_bash
+def test_setup_plan_preserves_existing_plan(plan_repo: Path) -> None:
+    """Rerun must not overwrite an existing plan.md."""
+    feat = plan_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    existing_content = "# My carefully authored plan\n\nDo not overwrite me.\n"
+    (feat / "plan.md").write_text(existing_content, encoding="utf-8")
+
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    # Plan must be unchanged
+    assert (feat / "plan.md").read_text(encoding="utf-8") == existing_content
+
+
+@requires_bash
+def test_setup_plan_skip_message_on_stderr_in_json_mode(plan_repo: Path) -> None:
+    """In --json mode, status messages must go to stderr, not stdout."""
+    feat = plan_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    (feat / "plan.md").write_text("# existing\n", encoding="utf-8")
+
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    # stdout must be valid JSON (no status messages mixed in)
+    data = json.loads(result.stdout)
+    assert "IMPL_PLAN" in data
+    # The skip message should be on stderr
+    assert "already exists" in result.stderr
+
+
+@requires_bash
+def test_setup_plan_json_parseable_on_first_run(plan_repo: Path) -> None:
+    """In --json mode, first-run stdout must be parseable JSON (no status on stdout)."""
+    script = plan_repo / ".specify" / "scripts" / "bash" / "setup-plan.sh"
+    result = subprocess.run(
+        ["bash", str(script), "--json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    assert "IMPL_PLAN" in data
+    assert "Copied plan template" in result.stderr
+
+
+# ── PowerShell tests ──────────────────────────────────────────────────────
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_setup_plan_creates_plan_when_missing(plan_repo: Path) -> None:
+    """First run must create plan.md from the template."""
+    script = plan_repo / ".specify" / "scripts" / "powershell" / "setup-plan.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    data = json.loads(result.stdout)
+    plan_path = Path(data["IMPL_PLAN"])
+    assert plan_path.is_file()
+    content = plan_path.read_text(encoding="utf-8")
+    assert len(content) > 0
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _POWERSHELL), reason="no PowerShell available")
+def test_ps_setup_plan_preserves_existing_plan(plan_repo: Path) -> None:
+    """Rerun must not overwrite an existing plan.md."""
+    feat = plan_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    existing_content = "# My carefully authored plan\n\nDo not overwrite me.\n"
+    (feat / "plan.md").write_text(existing_content, encoding="utf-8")
+
+    script = plan_repo / ".specify" / "scripts" / "powershell" / "setup-plan.ps1"
+    exe = "pwsh" if HAS_PWSH else _POWERSHELL
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json"],
+        cwd=plan_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=_clean_env(),
+    )
+    assert result.returncode == 0, result.stderr
+    assert (feat / "plan.md").read_text(encoding="utf-8") == existing_content
+    # stdout must be valid JSON (no status messages mixed in)
+    data = json.loads(result.stdout)
+    assert "IMPL_PLAN" in data
+    # The skip message should be on stderr
+    assert "already exists" in result.stderr