diff --git a/scripts/bash/check-prerequisites.sh b/scripts/bash/check-prerequisites.sh
index 2c1b8e1351..4b70070868 100644
--- a/scripts/bash/check-prerequisites.sh
+++ b/scripts/bash/check-prerequisites.sh
@@ -79,7 +79,11 @@ SCRIPT_DIR="$(CDPATH="" cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 source "$SCRIPT_DIR/common.sh"
 
 # Get feature paths
-_paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+if $PATHS_ONLY; then
+    _paths_output=$(get_feature_paths --no-persist) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+else
+    _paths_output=$(get_feature_paths) || { echo "ERROR: Failed to resolve feature paths" >&2; exit 1; }
+fi
 eval "$_paths_output"
 unset _paths_output
 
diff --git a/scripts/bash/common.sh b/scripts/bash/common.sh
index 70ab89b013..3a46b9b74e 100644
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -152,6 +152,11 @@ _persist_feature_json() {
 }
 
 get_feature_paths() {
+    local no_persist=false
+    if [[ "${1:-}" == "--no-persist" ]]; then
+        no_persist=true
+    fi
+
     # Split decl/assignment so a SPECIFY_INIT_DIR validation failure in
     # get_repo_root propagates as a hard error instead of being masked by `local`.
     local repo_root
@@ -169,7 +174,9 @@ get_feature_paths() {
         # Normalize relative paths to absolute under repo root
         [[ "$feature_dir" != /* ]] && feature_dir="$repo_root/$feature_dir"
         # Persist to feature.json so future sessions without the env var still work
-        _persist_feature_json "$repo_root" "$SPECIFY_FEATURE_DIRECTORY"
+        if [[ "$no_persist" == "false" ]]; then
+            _persist_feature_json "$repo_root" "$SPECIFY_FEATURE_DIRECTORY"
+        fi
     elif [[ -f "$repo_root/.specify/feature.json" ]]; then
         local _fd
         _fd=$(read_feature_json_feature_directory "$repo_root")
diff --git a/scripts/powershell/check-prerequisites.ps1 b/scripts/powershell/check-prerequisites.ps1
index bb60e52c85..a750fd8015 100644
--- a/scripts/powershell/check-prerequisites.ps1
+++ b/scripts/powershell/check-prerequisites.ps1
@@ -57,7 +57,11 @@ EXAMPLES:
 . "$PSScriptRoot/common.ps1"
 
 # Get feature paths
-$paths = Get-FeaturePathsEnv
+$paths = if ($PathsOnly) {
+    Get-FeaturePathsEnv -NoPersist
+} else {
+    Get-FeaturePathsEnv
+}
 
 # If paths-only mode, output paths and exit (no validation)
 if ($PathsOnly) {
diff --git a/scripts/powershell/common.ps1 b/scripts/powershell/common.ps1
index f56fc26577..ce3824a970 100644
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -143,6 +143,10 @@ function Save-FeatureJson {
 }
 
 function Get-FeaturePathsEnv {
+    param(
+        [switch]$NoPersist
+    )
+
     $repoRoot = Get-RepoRoot
     $currentBranch = Get-CurrentBranch
 
@@ -158,7 +162,9 @@ function Get-FeaturePathsEnv {
             $featureDir = Join-Path $repoRoot $featureDir
         }
         # Persist to feature.json so future sessions without the env var still work
-        Save-FeatureJson -RepoRoot $repoRoot -FeatureDirectory $env:SPECIFY_FEATURE_DIRECTORY
+        if (-not $NoPersist) {
+            Save-FeatureJson -RepoRoot $repoRoot -FeatureDirectory $env:SPECIFY_FEATURE_DIRECTORY
+        }
     } elseif (Test-Path $featureJson) {
         $featureJsonRaw = Get-Content -LiteralPath $featureJson -Raw
         try {
diff --git a/tests/test_check_prerequisites_paths_only.py b/tests/test_check_prerequisites_paths_only.py
index 03e2fc6e8b..2d1c8c6b83 100644
--- a/tests/test_check_prerequisites_paths_only.py
+++ b/tests/test_check_prerequisites_paths_only.py
@@ -17,7 +17,11 @@
 CHECK_PREREQS_PS = PROJECT_ROOT / "scripts" / "powershell" / "check-prerequisites.ps1"
 
 HAS_PWSH = shutil.which("pwsh") is not None
-_WINDOWS_POWERSHELL = (shutil.which("powershell.exe") or shutil.which("powershell")) if os.name == "nt" else None
+_WINDOWS_POWERSHELL = (
+    (shutil.which("powershell.exe") or shutil.which("powershell"))
+    if os.name == "nt"
+    else None
+)
 
 
 def _install_bash_scripts(repo: Path) -> None:
@@ -141,6 +145,41 @@ def test_paths_only_text_mode_on_non_spec_branch(prereq_repo: Path) -> None:
     assert "FEATURE_DIR:" in result.stdout
 
 
+@requires_bash
+def test_paths_only_does_not_overwrite_feature_json(prereq_repo: Path) -> None:
+    """--paths-only must not rewrite .specify/feature.json when env differs."""
+    common = (prereq_repo / ".specify" / "scripts" / "bash" / "common.sh").read_text(
+        encoding="utf-8"
+    )
+    script_text = (
+        prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    ).read_text(encoding="utf-8")
+    assert "SPECIFY_NO_PERSIST_FEATURE_JSON" not in common
+    assert "get_feature_paths --no-persist" in script_text
+
+    feat = prereq_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True, exist_ok=True)
+    _write_feature_json(prereq_repo)
+    before = (prereq_repo / ".specify" / "feature.json").read_text(encoding="utf-8")
+    script = prereq_repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    env = _clean_env()
+    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/999-temp"
+    result = subprocess.run(
+        ["bash", str(script), "--json", "--paths-only"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=env,
+    )
+    assert result.returncode == 0, result.stderr
+    assert (prereq_repo / ".specify" / "feature.json").read_text(
+        encoding="utf-8"
+    ) == before
+    data = json.loads(result.stdout)
+    assert data["FEATURE_DIR"].endswith("specs/999-temp")
+
+
 @requires_bash
 def test_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
     """Without --paths-only, feature directory validation must still fail on main."""
@@ -160,13 +199,17 @@ def test_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
 # ── PowerShell tests ──────────────────────────────────────────────────────
 
 
-@pytest.mark.skipif(not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available")
+@pytest.mark.skipif(
+    not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available"
+)
 def test_ps_paths_only_succeeds_on_non_spec_branch(prereq_repo: Path) -> None:
     """-PathsOnly must return paths when feature.json pins the feature dir."""
     feat = prereq_repo / "specs" / "001-my-feature"
     feat.mkdir(parents=True, exist_ok=True)
     _write_feature_json(prereq_repo)
-    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    script = (
+        prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    )
     exe = "pwsh" if HAS_PWSH else _WINDOWS_POWERSHELL
     result = subprocess.run(
         [exe, "-NoProfile", "-File", str(script), "-Json", "-PathsOnly"],
@@ -183,7 +226,9 @@ def test_ps_paths_only_succeeds_on_non_spec_branch(prereq_repo: Path) -> None:
     assert "FEATURE_DIR" in data
 
 
-@pytest.mark.skipif(not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available")
+@pytest.mark.skipif(
+    not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available"
+)
 def test_ps_paths_only_succeeds_on_spec_branch(prereq_repo: Path) -> None:
     """-PathsOnly must also work when feature.json and SPECIFY_FEATURE agree."""
     subprocess.run(
@@ -194,7 +239,9 @@ def test_ps_paths_only_succeeds_on_spec_branch(prereq_repo: Path) -> None:
     feat = prereq_repo / "specs" / "001-my-feature"
     feat.mkdir(parents=True, exist_ok=True)
     _write_feature_json(prereq_repo)
-    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    script = (
+        prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    )
     exe = "pwsh" if HAS_PWSH else _WINDOWS_POWERSHELL
     env = _clean_env()
     env["SPECIFY_FEATURE"] = "001-my-feature"
@@ -211,10 +258,54 @@ def test_ps_paths_only_succeeds_on_spec_branch(prereq_repo: Path) -> None:
     assert "FEATURE_DIR" in data
 
 
-@pytest.mark.skipif(not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available")
+@pytest.mark.skipif(
+    not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available"
+)
+def test_ps_paths_only_does_not_overwrite_feature_json(prereq_repo: Path) -> None:
+    """-PathsOnly must not rewrite .specify/feature.json when env differs."""
+    common = (
+        prereq_repo / ".specify" / "scripts" / "powershell" / "common.ps1"
+    ).read_text(encoding="utf-8")
+    script_text = (
+        prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    ).read_text(encoding="utf-8")
+    assert "SPECIFY_NO_PERSIST_FEATURE_JSON" not in common
+    assert "Get-FeaturePathsEnv -NoPersist" in script_text
+
+    feat = prereq_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True, exist_ok=True)
+    _write_feature_json(prereq_repo)
+    before = (prereq_repo / ".specify" / "feature.json").read_text(encoding="utf-8")
+    script = (
+        prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    )
+    exe = "pwsh" if HAS_PWSH else _WINDOWS_POWERSHELL
+    env = _clean_env()
+    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/999-temp"
+    result = subprocess.run(
+        [exe, "-NoProfile", "-File", str(script), "-Json", "-PathsOnly"],
+        cwd=prereq_repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=env,
+    )
+    assert result.returncode == 0, result.stderr
+    assert (prereq_repo / ".specify" / "feature.json").read_text(
+        encoding="utf-8"
+    ) == before
+    data = json.loads(result.stdout)
+    assert data["FEATURE_DIR"].replace("\\", "/").endswith("specs/999-temp")
+
+
+@pytest.mark.skipif(
+    not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available"
+)
 def test_ps_normal_mode_still_validates_branch(prereq_repo: Path) -> None:
     """Without -PathsOnly, feature directory validation must still fail on main."""
-    script = prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    script = (
+        prereq_repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    )
     exe = "pwsh" if HAS_PWSH else _WINDOWS_POWERSHELL
     result = subprocess.run(
         [exe, "-NoProfile", "-File", str(script), "-Json"],