diff --git a/scripts/bash/check-prerequisites.sh b/scripts/bash/check-prerequisites.sh
index 2c1b8e1351..5d2eb08183 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 $PATHS_ONLY; then
+    _paths_output=$(SPECIFY_NO_PERSIST_FEATURE_JSON=1 get_feature_paths) || { 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 3ea66a652d..cf565877d4 100644
--- a/scripts/bash/common.sh
+++ b/scripts/bash/common.sh
@@ -95,6 +95,10 @@ _persist_feature_json() {
     local feature_dir_value="$2"
     local fj="$repo_root/.specify/feature.json"
 
+    if [[ "${SPECIFY_NO_PERSIST_FEATURE_JSON:-}" == "1" ]]; then
+        return 0
+    fi
+
     # Strip repo_root prefix if the value is absolute and under repo_root
     if [[ "$feature_dir_value" == "$repo_root/"* ]]; then
         feature_dir_value="${feature_dir_value#"$repo_root/"}"
diff --git a/scripts/powershell/check-prerequisites.ps1 b/scripts/powershell/check-prerequisites.ps1
index bb60e52c85..bd63e9094e 100644
--- a/scripts/powershell/check-prerequisites.ps1
+++ b/scripts/powershell/check-prerequisites.ps1
@@ -57,6 +57,9 @@ EXAMPLES:
 . "$PSScriptRoot/common.ps1"
 
 # Get feature paths
+if ($PathsOnly) {
+    $env:SPECIFY_NO_PERSIST_FEATURE_JSON = '1'
+}
 $paths = Get-FeaturePathsEnv
 
 # If paths-only mode, output paths and exit (no validation)
diff --git a/scripts/powershell/common.ps1 b/scripts/powershell/common.ps1
index 35406d3f66..bfaf4b1025 100644
--- a/scripts/powershell/common.ps1
+++ b/scripts/powershell/common.ps1
@@ -60,6 +60,10 @@ function Save-FeatureJson {
         [Parameter(Mandatory = $true)][string]$FeatureDirectory
     )
 
+    if ($env:SPECIFY_NO_PERSIST_FEATURE_JSON -eq '1') {
+        return
+    }
+
     # Strip repo root prefix if the value is absolute and under repo root.
     # Use case-insensitive comparison on Windows only (case-sensitive filesystems elsewhere).
     $prefix = $RepoRoot + [System.IO.Path]::DirectorySeparatorChar
diff --git a/tests/test_check_prerequisites_paths_only.py b/tests/test_check_prerequisites_paths_only.py
index 03e2fc6e8b..3f376ae6ee 100644
--- a/tests/test_check_prerequisites_paths_only.py
+++ b/tests/test_check_prerequisites_paths_only.py
@@ -141,6 +141,33 @@ 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."""
+    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."""
@@ -211,6 +238,34 @@ 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")
+def test_ps_paths_only_does_not_overwrite_feature_json(prereq_repo: Path) -> None:
+    """-PathsOnly must not rewrite .specify/feature.json when env differs."""
+    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."""