certctl/docs/reference/protocols/scep-intune.md

Microsoft Intune SCEP enrollment via certctl

Last reviewed: 2026-05-05

Status (this document): Phase 11 of the SCEP RFC 8894 + Intune master bundle. The behavior described here is shipped on master and exercised end-to-end by internal/api/handler/scep_intune_e2e_test.go. The bundle is V2-free (community edition) — Conditional-Access compliance gating, native Microsoft Graph integration, and per-tenant trust anchors are documented under Limitations as V3-Pro features.

TL;DR

certctl is a drop-in NDES replacement for Microsoft Intune SCEP fleets. Intune-managed devices keep using the existing Intune Certificate Connector; only the SCEP server URL changes. certctl validates the Connector's signed challenge using its installation signing cert (no Microsoft API calls — the Connector already did that), binds the device claim to the inbound CSR, and issues through whichever certctl issuer connector you have configured (local CA, Vault, EJBCA, ADCS, etc.).

What you get over NDES:

• Per-profile SCEP endpoints (/scep/corp vs. /scep/iot etc.) so a single certctl deploy serves multiple device fleets with distinct challenge passwords + trust anchors.
• Audit log entries with the device GUID, claim subject, and CSR binding details — much better forensics than NDES + IIS logs.
• Trust anchor reload via SIGHUP (no service restart) when the Connector signing cert rotates.
• A built-in admin GUI tab (Intune Monitoring) showing per-profile enrollment counters, trust-anchor expiry countdowns, and the recent failures table.
• Per-device rate limit (sliding window log keyed by Subject + Issuer) that catches a compromised Connector signing key issuing many different valid challenges for the same device.

Architecture

flowchart LR
    Cloud["Intune cloud<br/>(Microsoft)"]
    Connector["Intune Certificate Connector<br/>(customer infra)"]
    Server["certctl SCEP server<br/>(you)"]
    Issuer["issuer connector<br/>(local CA / Vault / EJBCA / …)"]
    Cloud --> Connector --> Server --> Issuer

certctl replaces NDES, not the Connector. The Intune Certificate Connector is the bridge between the Intune cloud and your on-prem PKI; Microsoft installs and maintains it. What you replace is the Network Device Enrollment Service (NDES) — the SCEP server historically deployed on a Windows host, sitting between the Connector and an Active Directory Certificate Services CA. certctl sits in exactly that slot and speaks SCEP RFC 8894 to the Connector.

What certctl validates per request

For every Intune-flavored SCEP request the dispatcher in internal/service/scep.go::dispatchIntuneChallenge walks the following gates in order. A failure on any gate produces a CertRep PKIMessage with the documented pkiStatus/failInfo codes (per RFC 8894 §3.2.1.4.5) and increments the corresponding metric counter.

1. Shape pre-check — looksIntuneShaped(challengePassword): length > 200 + exactly two dots. False positives are fine; false negatives on real Intune challenges would route them to the static compare and reject. The pre-check just decides whether to invoke the full validator.
2. JWS signature — intune.ValidateChallenge re-derives the signing input from the raw on-wire bytes (per RFC 7515 §3.1, NOT re-base64-encoded segments) and verifies against every cert in the trust anchor pool. Supports RS256 and ES256 (both fixed-width r||s and ASN.1-DER form). Explicitly rejects alg=none and HMAC algs.
3. Version dispatch — extracts the version claim from the payload prelude. v1 (current Connector format, no version key) routes to unmarshalChallengeV1. Future v2 plugs in a sibling parser without touching the validator.
4. Time bounds — now+tolerance ≥ iat AND now-tolerance < exp. The ±tolerance window is configurable per profile via INTUNE_CLOCK_SKEW_TOLERANCE (default 60s, covers modest clock drift between the Connector host and certctl). Configurable cap on top via INTUNE_CHALLENGE_VALIDITY (defense-in-depth against a Connector that mints long-validity challenges). The validator refuses tolerance ≥ ChallengeValidity at startup-validation time to keep the cap meaningful.
5. Audience pin — claim.aud == INTUNE_AUDIENCE (skipped when INTUNE_AUDIENCE is empty for proxy/load-balancer scenarios).
6. CSR binding — claim.DeviceMatchesCSR(csr) checks set-equality between the claim's device_name / san_dns / san_rfc822 / san_upn and the CSR's CN + SANs. Set-equality means the CSR carries EXACTLY the claim's values, no extras and no missing.
7. Replay — intune.ReplayCache.CheckAndInsert rejects duplicates within the configured TTL. Sized for 100k entries (covers a ~25 RPS Intune fleet's steady-state).
8. Per-device rate limit — sliding window log keyed by (claim.Subject, claim.Issuer). Catches a compromised Connector issuing many DIFFERENT valid challenges for the same device. Default 3 enrollments per 24h covers legitimate first-cert + recovery + post-wipe.
9. Optional compliance check — V3-Pro plug-in seam (nil-default no-op). When set, the gate calls Microsoft Graph's compliance API and short-circuits non-compliant devices with FAILURE+BadRequest.

A request that passes all nine gates flows to processEnrollment, which builds the issuance request, calls the configured issuer connector, and emits a CertRep PKIMessage with the issued cert encrypted to the device's transient signing cert per RFC 8894 §3.3.2.

Migration from NDES + EJBCA (or NDES + ADCS)

The migration plan below is conservative — install certctl alongside your existing NDES so you can flip Intune profiles fleet-by-fleet without a flag day. Validated against a fresh docker compose up stack; the docker-compose.test.yml stack does not currently bake Intune in (Phase 10.2 ships a hermetic in-process e2e test instead), so the production validation step is a manual run-book item.

1. Install certctl alongside existing NDES. Stand up the certctl server on a separate host (or as a Kubernetes deployment) reachable from the Connector host. Use the existing operator-run-book in docs/tls.md for the TLS bootstrap.

2. Configure a per-profile SCEP endpoint. Pick a path id (e.g. corp — referenced as <NAME> below; the value gets uppercased for the env-var key and lowercased for the URL path) and set:

   CERTCTL_SCEP_ENABLED=true
   CERTCTL_SCEP_PROFILES=corp
   CERTCTL_SCEP_PROFILE_<NAME>_ISSUER_ID=iss-local           # or your existing issuer
   CERTCTL_SCEP_PROFILE_<NAME>_CHALLENGE_PASSWORD=<random>   # Intune still requires this
   CERTCTL_SCEP_PROFILE_<NAME>_RA_CERT_PATH=/etc/certctl/ra-corp.pem
   CERTCTL_SCEP_PROFILE_<NAME>_RA_KEY_PATH=/etc/certctl/ra-corp.key
   

   The endpoint will be served at https://certctl.example.com/scep/corp — the URL path uses the lowercased name and the env-var keys use the uppercased form. Concrete env-var name mappings are listed in features.md.

3. Extract the Intune Connector's signing cert. On the Connector host (Windows), the Connector's installation creates a self-signed cert in the local machine's Personal cert store with subject CN=Microsoft Intune Certificate Connector (path documented by Microsoft — see Microsoft Learn link in the Microsoft support statement below). Export the public cert (no private key) as a base64 .cer file.

4. Configure the trust anchor. Copy the .cer to the certctl host (or mount via your secret manager) and set:

   CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_ENABLED=true
   CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_CONNECTOR_CERT_PATH=/etc/certctl/intune-corp.pem
   CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_AUDIENCE=https://certctl.example.com/scep/corp
   CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_CHALLENGE_VALIDITY=60m
   CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_CLOCK_SKEW_TOLERANCE=60s   # ±tolerance on iat/exp; raise on poorly-NTP-synced fleets, lower to enforce strict time
   CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_PER_DEVICE_RATE_LIMIT_24H=3
   

   Restart certctl. The startup preflight refuses to boot if the trust anchor file is missing, unparseable, or contains an expired cert — failure is loud at boot rather than silent at request time.

5. Configure the issuer connector. If you're keeping EJBCA, point CERTCTL_SCEP_PROFILE_<NAME>_ISSUER_ID at your EJBCA issuer profile (see docs/connectors.md). For a clean cut-over to the built-in local CA, follow docs/tls.md to bootstrap a sub-CA cert.

6. Migrate one Intune SCEP profile to certctl. In the Intune admin center, edit the SCEP profile for a small canary device group and update the SCEP server URL to https://certctl.example.com/scep/corp. Push the profile and wait for the canary devices to rotate (24-48h).

7. Verify enrollment. Open the certctl admin GUI's SCEP Intune Monitoring tab and watch the success counter tick on the corp profile card. The recent failures table surfaces any rejected enrollments with the exact reason (e.g. signature_invalid, claim_mismatch).

8. Roll out the rest of the fleet. Once the canary is clean, migrate the remaining Intune SCEP profiles in batches.

9. Decommission NDES. After all fleets are migrated and a few renewal cycles have completed cleanly, take down the NDES role and the IIS site. The existing certs continue to chain to your issuer; only the enrollment path changes.

Intune SCEP profile fields → certctl behavior

The Intune admin center's SCEP profile editor exposes a fixed set of fields. The mapping below is what each field controls relative to certctl's behavior.

Intune profile field	certctl behavior
Certificate type	Treated as device or user; surfaces in the claim's subject field (device GUID vs. user UPN). certctl doesn't gate on type; the issuer's certificate profile decides.
Subject name format	Drives the CSR's CN. The Intune Connector sets claim.device_name from this value; certctl's CSR-binding gate enforces equality.
Subject alternative name	Drives the CSR's SAN list. Intune supports DNS / RFC 822 / UPN; certctl's claim binding checks set-equality per dimension. Mismatches surface as ErrClaimSANDNSMismatch / _SANRFC822Mismatch / _SANUPNMismatch.
Certificate validity period	Honored by the issuer connector. certctl caps via the per-profile CertificateProfile.MaxTTLSeconds; the smaller of the two wins.
Key storage provider	Device-side concern (the Connector negotiates with the device's TPM / Software KSP). certctl never sees the device's private key — it only signs the CSR.
Key usage / Extended key usage	Honored by the issuer connector via the bound CertificateProfile.AllowedEKUs. CSRs requesting an EKU outside the allowed set are rejected by the crypto-policy gate (ValidateCSRAgainstProfile).
Hash algorithm	The CSR's signature hash (SHA-256 typical). The SCEP GetCACaps advertises SHA-256 + SHA-512; the device picks.
SCEP server URL	The endpoint URL the Connector posts to. Set to https://certctl.example.com/scep/<profile-name>.

Trust anchor extraction

The Intune Certificate Connector self-signs an installation cert at install time. To configure certctl, extract this cert (PUBLIC ONLY, no private key) as PEM:

1. On the Connector host (Windows), open certlm.msc (Local Machine Certificate Manager).
2. Navigate to Personal → Certificates. Find the cert with subject CN=Microsoft Intune Certificate Connector.
3. Right-click → All Tasks → Export. Choose No, do not export the private key. Format: Base-64 encoded X.509 (.CER).
4. Copy the resulting .cer file to the certctl host. Rename to .pem (the bytes are identical; certctl's PEM loader accepts either extension).
5. Set CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_CONNECTOR_CERT_PATH to the file path.
6. If you have multiple Connectors in HA, repeat steps 1-3 on each and concatenate the PEM blocks into one bundle file.

When the operator rotates the Connector signing cert (typically once every few years per Microsoft's Connector lifecycle), repeat the extraction, overwrite the on-disk file, then send SIGHUP to the certctl process. The trust holder swaps atomically; bad files (parse error, expired cert) keep the OLD pool in place so a half-rotation doesn't take Intune enrollment down.

Troubleshooting

The dispatcher emits a typed metric label per failure mode plus a matching audit-log entry. The table below maps the label to the most common root cause and the operator action.

Counter label	Symptom	Root cause + fix
signature_invalid	Every enrollment from a specific profile failing	Trust anchor mismatch — the Connector's signing cert was rotated and certctl wasn't reloaded. Re-extract the cert (trust anchor extraction), overwrite the file, send SIGHUP.
claim_mismatch	Some enrollments from one Intune SCEP profile failing	The Intune SCEP profile's SAN config doesn't match what the device CSR actually has. Compare the recent failures table's claim row to the device's CSR; usually a SAN format mismatch (e.g. claim wants UPN, CSR has DNS).
expired	All enrollments failing on a date boundary	Either clock skew between the Connector host and certctl (NTP both ends) OR the Connector's signing cert is past NotAfter. The certctl preflight catches an expired trust anchor at boot; check the Monitoring tab's expiry countdown.
not_yet_valid	All enrollments failing	Reverse clock skew (certctl's clock is BEHIND the Connector's). Sync via NTP.
wrong_audience	All enrollments from a profile failing	INTUNE_AUDIENCE doesn't match the URL the Connector is configured to call. Either fix INTUNE_AUDIENCE to match the operator URL, or unset it (defense-in-depth then disabled — the claim's exp + sig still gate).
replay	Sporadic per-device failures, mostly during retries	The device retried the SAME challenge after the first one failed. The replay cache TTL is INTUNE_CHALLENGE_VALIDITY (default 60m). Either widen the device's retry window (Intune-side) or shorten validity.
rate_limited	A specific device hitting 429-equivalent failures	The device exceeded INTUNE_PER_DEVICE_RATE_LIMIT_24H (default 3). If legitimate (post-wipe + recovery + first-cert all in 24h), bump the cap. If suspicious, this is the limiter doing its job — investigate the device.
unknown_version	Sudden onset of failures across the entire fleet	Microsoft shipped a new Connector version with a version claim certctl doesn't understand. Open an issue on the certctl repo with the failing claim payload (anonymized); the parser dispatcher accepts new versions in ~30 LoC.
malformed	Sporadic, low-volume	Malformed challenge bytes — almost always a network proxy mangling the request body, or the Connector logging itself out mid-handshake. Capture a packet trace; the Connector should re-emit on the next device retry.
compliance_failed	V3-Pro only	The pluggable compliance check returned non-compliant. The audit-log details carries the reason string from Microsoft Graph. V2 deployments never see this counter tick.

Operational monitoring (SCEP Administration → Intune Monitoring tab)

The admin GUI surface for SCEP lives at /scep and is structured as three tabs: Profiles (default landing — every configured SCEP profile, lean cards with always-present fields), Intune Monitoring (the Intune-specific deep-dive described below), and Recent Activity (full SCEP audit log filter). Operators monitoring an Intune deployment spend most of their time on the Intune Monitoring tab, deep-linkable via /scep?tab=intune or the legacy alias /scep/intune. The Profiles tab gives the at-a-glance per-profile health (RA cert expiry, mTLS status, Intune enabled/disabled badge, challenge-password-set indicator) and a "View Intune details →" link from each Intune-enabled card that switches into this tab filtered to that profile.

The Intune Monitoring tab shows:

• Per-profile cards — one card per SCEP profile, with the trust anchor expiry countdown badge:
  • green ≥ 30 days remaining
  • amber 7-30 days remaining (rotate soon)
  • red < 7 days remaining
  • EXPIRED past NotAfter
• Live counters — the per-status enrollment counts polled every 30s. The order in the grid puts success first (vanity) and failure modes after.
• Recent failures table — the last 50 audit-log events with action scep_pkcsreq_intune or scep_renewalreq_intune, sorted by timestamp descending. Polled every 60s.
• Trust anchor reload button — confirms via modal then issues POST /api/v1/admin/scep/intune/reload-trust (the SIGHUP-equivalent). Bad reloads keep the OLD pool in place; the modal stays open with the underlying error so the operator can correct the file and retry.

Three admin endpoints back the page:

• GET /api/v1/admin/scep/profiles — per-profile snapshot for the Profiles tab; surfaces RA cert subject + NotAfter + days-to-expiry, mTLS sibling-route status + bundle path, challenge-password-set flag, and an optional intune sub-block for Intune-enabled profiles.
• GET /api/v1/admin/scep/intune/stats — Intune-specific deep-dive for the Intune Monitoring tab; per-status counters + trust anchor pool details. Backward-compat shape preserved from Phase 9.
• POST /api/v1/admin/scep/intune/reload-trust — SIGHUP-equivalent trust anchor reload, body {"path_id": "<pathID>"}.

All three are M-008 admin-gated. Non-admin Bearer callers get HTTP 403

• a clear message; the GUI hides the page entirely for non-admin users (UX hint; server-side enforcement is independent).

Recommended alert thresholds

The counters are exposed in the GUI as snapshots; if you wrap them in a Prometheus exporter (V3-Pro plug-in seam — V2 doesn't ship a /metrics surface today), reasonable starting thresholds:

• signature_invalid rate > 0 for > 5 minutes → page on-call. The trust anchor is stale; the operator missed a SIGHUP after a Connector rotation.
• claim_mismatch rate > 0 sustained > 1 hour → notify (not page). An Intune SCEP profile is misconfigured; an admin needs to fix the SAN definition or the operator's CertificateProfile.
• replay rate climbing → notify. Either an aggressive retry policy on the device side OR active replay attempts. Cross-reference source IPs in the audit log.
• rate_limited for a single device > 1 per hour → notify. Either legitimate enrollment storm (post-wipe scenarios) or a compromised Connector signing key.
• Trust anchor days_to_expiry < 30 on any profile → notify; rotate the Connector's signing cert before the cliff.

Limitations

This bundle is V2-free. The following capabilities are deferred to V3-Pro:

• Native Microsoft Graph integration. certctl validates the Connector's signed challenge but doesn't call Microsoft's API directly — the Connector already did that. V3-Pro could ship a Graph client that pulls device-compliance state in addition to the challenge claim.
• Conditional Access compliance gating. The dispatcher exposes a nil-default ComplianceCheck hook. V3-Pro plugs in a Microsoft Graph compliance lookup before issuance; non-compliant devices fail with a typed compliance_failed failInfo.
• Per-tenant trust anchors. V2 has one trust anchor pool per SCEP profile; V3-Pro could support per-AAD-tenant anchor scoping for MSPs running shared certctl deployments across customers.
• OCSP stapling at SCEP-response time. The CertRep doesn't carry a stapled OCSP response today; certificate validators look up OCSP via the id-pkix-ocsp extension on the issued cert. V3-Pro could staple inline.
• Auto-discovery of the Connector signing cert. V2 requires the operator to extract the cert manually and configure the path. V3-Pro could pull from a Microsoft-published endpoint (with the appropriate trust constraints).

These deferrals are deliberate, not oversights. The V2 surface covers every operationally-required path for a single-tenant enterprise replacing NDES; V3-Pro adds the multi-tenant + native-API features procurement teams sometimes ask for.

Microsoft support statement

Microsoft documents the Intune Certificate Connector as RFC-8894-compliant and supports its use against any RFC 8894 SCEP server. The relevant Microsoft Learn pages:

• Intune Certificate Connector overview — documents the Connector's architecture and explicitly notes it speaks RFC-8894-compliant SCEP.
• Use SCEP certificate profiles in Intune — the operator-facing setup guide, with the SCEP server URL field the migration playbook above edits.
• Validate setup of Intune Certificate Connector — the install-validation checklist; useful when troubleshooting Connector-side failures vs. certctl-side failures.

certctl's role per Microsoft's framing: a third-party SCEP server that the Connector posts to. Microsoft supports this topology; only certctl's own RFC 8894 implementation is in scope for certctl support. The end-to-end Connector → certctl → issuer flow is exercised in internal/api/handler/scep_intune_e2e_test.go and the golden-file fixtures in internal/scep/intune/testdata/.

Related docs

• legacy-est-scep.md — the per-profile SCEP setup guide + RFC 8894 reference + mTLS sibling route. Read this first if you're not already running certctl SCEP for non-Intune fleets.
• architecture.md — overall control-plane architecture; Security Model section calls out the Intune trust anchor as a sensitive operator-configured surface.
• features.md — every CERTCTL_* env var, including the per-profile CERTCTL_SCEP_PROFILE_<NAME>_INTUNE_* family.
• tls.md — TLS bootstrap for the certctl control plane; prerequisite for any production deploy.