diff --git a/CLAUDE.md b/CLAUDE.md
index 371bff8..cb60119 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -120,6 +120,16 @@ src/vaultctl/
 - `_previous` backup keys are excluded; field names with non-identifier
   characters get quoted
 
+**8. Schema-aware `set` (#40 phase 3):**
+- After computing the new vault data, `set` validates it against
+  `.vaultctl/vault.cue` if both the baseline and `cue` exist
+- `_previous` backup keys are stripped from the validation input — they aren't
+  in the schema by design, and pre-existing backups must not look like drift
+  for unrelated changes
+- Default behaviour is interactive: prompt to extend, then prompt to proceed
+  with drift. `--extend-schema` / `--no-extend-schema` short-circuit both
+  prompts; `--force` alone implies `--no-extend-schema`
+
 ### CLI Commands
 
 | Command | Description |
diff --git a/README.md b/README.md
index 4be31cd..b2fdf25 100644
--- a/README.md
+++ b/README.md
@@ -160,6 +160,27 @@ vaultctl schema sync --apply   # rewrite the baseline to match the vault
 
 `schema sync` re-derives the schema from the current vault content and compares it to `.vaultctl/vault.cue`. Without `--apply` it prints a unified diff and exits non-zero; with `--apply` it rewrites the baseline. `vault.constraints.cue` is never touched — CUE merges it back in at validation time.
 
+**Schema-aware `set`:**
+
+When a baseline exists, `vaultctl set` checks the new vault content against it before encrypting. If a value introduces structure the schema doesn't cover (e.g. a new key), `set` shows the diff and asks whether to extend the baseline:
+
+```bash
+vaultctl set new_token "abc123"
+# → Schema does not cover this change:
+#   --- .vaultctl/vault.cue (current)
+#   +++ .vaultctl/vault.cue (inferred)
+#   ...
+#       +	new_token: string
+#   Extend .vaultctl/vault.cue with this change? [y/N]:
+```
+
+Flags for non-interactive use:
+- `--extend-schema` — extend silently.
+- `--no-extend-schema` — leave the baseline alone, accept drift (`vaultctl validate` will flag it later).
+- `--force` without either flag — same as `--no-extend-schema` (safer non-interactive default).
+
+Without a baseline or without the `cue` binary, the check is skipped entirely.
+
 **Without `cue` installed:** schema checks are skipped with a warning; the cross-consistency check still runs.
 
 ## Type Detection
diff --git a/src/vaultctl/cli.py b/src/vaultctl/cli.py
index 5b8809d..2bf2f27 100644
--- a/src/vaultctl/cli.py
+++ b/src/vaultctl/cli.py
@@ -478,6 +478,14 @@ def _output_base64_encoded(value: Any) -> None:
 @click.option("--backup/--no-backup", default=True, help="Save previous value as <key>_previous.")
 @click.option("--expires", default=None, help="Expiry date (YYYY-MM-DD) for vault-keys.yml.")
 @click.option("--force", is_flag=True, default=False, help="Skip confirmation prompts.")
+@click.option(
+    "--extend-schema/--no-extend-schema",
+    "extend_schema",
+    default=None,
+    help="If the new value introduces structure not in .vaultctl/vault.cue, "
+    "either extend it (--extend-schema) or skip the prompt and proceed with drift "
+    "(--no-extend-schema). Default: prompt interactively.",
+)
 @pass_ctx
 def set(
     vctx: VaultContext,
@@ -490,6 +498,7 @@ def set(
     backup: bool,
     expires: str | None,
     force: bool,
+    extend_schema: bool | None,
 ) -> None:
     """Set a vault key."""
     value = _resolve_set_value(value, use_prompt, from_file, from_base64, from_base64_file, key)
@@ -514,6 +523,8 @@ def set(
 
     data[key] = value
 
+    _apply_schema_aware_check(vctx, data, extend_schema=extend_schema, force=force)
+
     try:
         encrypt_vault(data, vctx.config.vault_file, vctx.password)
     except VaultError as exc:
@@ -753,6 +764,55 @@ def _print_detection_json(results: list[DetectionResult]) -> None:
     click.echo(json.dumps(items, indent=2))
 
 
+def _apply_schema_aware_check(
+    vctx: VaultContext,
+    new_data: dict[str, Any],
+    extend_schema: bool | None,
+    force: bool,
+) -> None:
+    """Validate `new_data` against the project schema baseline and react to drift.
+
+    Quietly skips the check when:
+    - the cue binary isn't available (validation isn't possible);
+    - no `.vaultctl/vault.cue` exists (no baseline to compare against).
+
+    Otherwise, if the new vault content fails validation against the baseline:
+    - prompt to extend the schema (default), or
+    - extend silently if `--extend-schema` was passed,
+    - or proceed with drift if `--no-extend-schema` (or `--force`) was passed.
+
+    Aborts the calling command with sys.exit(1) if the user declines both
+    options interactively. The caller has not yet written the vault, so abort
+    leaves it unchanged.
+    """
+    baseline = vctx.config.config_dir / ".vaultctl" / "vault.cue"
+    if not (cue_available() and baseline.is_file()):
+        return
+
+    # The schema deliberately excludes `_previous` backup keys (see
+    # infer_vault_schema). Strip them before validation so the schema check
+    # only reacts to the change being set, not to pre-existing backups.
+    check_data = {k: v for k, v in new_data.items() if not k.endswith("_previous")}
+    if not validate_vault_data(check_data, override=baseline):
+        return
+
+    click.echo("Schema does not cover this change:", err=True)
+    _, current, fresh = compute_schema_drift(check_data, baseline)
+    click.echo(render_schema_diff(current, fresh, str(baseline)), err=True)
+
+    decision = extend_schema
+    if decision is None:
+        # If --force is set with no explicit schema flag, pick the safer
+        # non-interactive default: leave drift; user notices via `validate`.
+        decision = False if force else click.confirm("Extend .vaultctl/vault.cue with this change?", default=False)
+
+    if decision:
+        baseline.write_text(fresh, encoding="utf-8")
+        click.echo(f"Updated {baseline}.")
+    elif not force:
+        click.confirm("Proceed without updating schema?", default=False, abort=True)
+
+
 def _resolve_set_value(
     value: str | None,
     use_prompt: bool,
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 308cd75..c393414 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -855,3 +855,90 @@ def test_schema_sync_apply_updates_baseline(runner, cli_env, tmp_path):
     follow_up = runner.invoke(main, ["schema", "sync"])
     assert follow_up.exit_code == 0, follow_up.output
     assert "No drift" in follow_up.output
+
+
+# --- schema-aware set (#40 phase 3) ---
+
+
+def test_set_skips_schema_check_when_no_baseline(runner, cli_env):
+    """Without a baseline, set behaves exactly as before."""
+    result = runner.invoke(main, ["set", "brand_new_key", "v", "--force", "--no-backup"])
+    assert result.exit_code == 0, result.output
+    assert "Schema does not cover" not in result.output
+
+
+def test_set_silent_when_key_already_in_schema(runner, cli_env):
+    """Modifying an existing key keeps the schema covered."""
+    runner.invoke(main, ["schema", "infer"])
+    result = runner.invoke(main, ["set", "test_key", "new_string_value", "--force", "--no-backup"])
+    assert result.exit_code == 0, result.output
+    assert "Schema does not cover" not in result.output
+
+
+def test_set_extend_schema_flag_writes_baseline(runner, cli_env):
+    """--extend-schema auto-extends the baseline without prompting."""
+    runner.invoke(main, ["schema", "infer"])
+    result = runner.invoke(
+        main,
+        ["set", "fresh_key", "fresh_value", "--force", "--no-backup", "--extend-schema"],
+    )
+    assert result.exit_code == 0, result.output
+    assert "Updated" in result.output
+
+    # The new key should now be part of the schema, so a sync reports no drift.
+    sync = runner.invoke(main, ["schema", "sync"])
+    assert sync.exit_code == 0, sync.output
+    assert "No drift" in sync.output
+
+
+def test_set_no_extend_schema_proceeds_with_drift(runner, cli_env):
+    """--no-extend-schema skips the prompt and accepts the resulting drift."""
+    runner.invoke(main, ["schema", "infer"])
+    result = runner.invoke(
+        main,
+        ["set", "another_fresh_key", "v", "--force", "--no-backup", "--no-extend-schema"],
+    )
+    assert result.exit_code == 0, result.output
+    assert "Updated" not in result.output  # baseline NOT updated
+
+    # Drift should be reported by sync.
+    sync = runner.invoke(main, ["schema", "sync"])
+    assert sync.exit_code == 1
+    assert "another_fresh_key" in sync.output
+
+
+def test_set_force_without_flag_defaults_to_no_extend(runner, cli_env):
+    """--force alone (no schema flag) leaves drift instead of prompting."""
+    runner.invoke(main, ["schema", "infer"])
+    result = runner.invoke(main, ["set", "force_only_key", "v", "--force", "--no-backup"])
+    assert result.exit_code == 0, result.output
+    # Schema notice still printed (so the user can see it in CI logs)
+    assert "Schema does not cover" in result.output
+    # But baseline not updated
+    assert "Updated" not in result.output
+
+
+def test_set_interactive_accept_extend(runner, cli_env):
+    """Interactive: user types 'y' to extend schema."""
+    runner.invoke(main, ["schema", "infer"])
+    result = runner.invoke(
+        main,
+        ["set", "interactive_key", "v", "--no-backup"],
+        input="y\n",  # answer "yes" to "Extend .vaultctl/vault.cue with this change?"
+    )
+    assert result.exit_code == 0, result.output
+    assert "Updated" in result.output
+
+
+def test_set_interactive_decline_extend_decline_proceed_aborts(runner, cli_env):
+    """Interactive: decline both prompts → abort, vault unchanged."""
+    runner.invoke(main, ["schema", "infer"])
+    result = runner.invoke(
+        main,
+        ["set", "abort_key", "v", "--no-backup"],
+        input="n\nn\n",  # decline extend, decline proceed
+    )
+    assert result.exit_code != 0
+    # Vault should not contain the key
+    after = runner.invoke(main, ["get", "abort_key"])
+    assert after.exit_code == 1  # not found