Appendix A — Cloud PKI and CBA Deployment Checklists

Two working checklists, verified against Microsoft documentation as of October 2026: deploying Microsoft Cloud PKI with Intune, and configuring Microsoft Entra certificate-based authentication through to domain cutover.

Appendix A — Cloud PKI and CBA Deployment Checklists

A checklist is only as good as the test at the end of each line.

NoteIn this appendix

Checklist A.1 deploys Microsoft Cloud PKI and the Intune profiles that use it, wave by wave. Checklist A.2 configures Microsoft Entra certificate-based authentication (CBA) from licensing through domain cutover and monitoring. Each line names an owner role and how to verify it. The reasoning behind each step is in Chapter 06 and Chapter 07; owner roles follow Chapter 05.

The waves are those of Chapter 07: Assess, Foundation, Pilot, Scale, Cutover, Decommission. Thresholds such as “99% of devices” are the program’s gates, not Microsoft requirements.

WarningIllustrative, not tested against a production tenant

The commands in this appendix are examples. They haven’t been run against a production forest or tenant. Read each one, run it first in a test scope, and review the output before you change anything.

A.1 Cloud PKI deployment checklist

Cloud PKI deployment checklist
# Task Wave Owner Verification
1 Confirm the tenant’s Cloud PKI entitlement: an add-on subscription to Intune Plan 1 or Plan 2, or (commercial tenants, from July 2026) Microsoft 365 E5 or E7. For a GCC tenant, confirm with licensing; Government packaging follows the enterprise plans subject to compliance requirements.12 Foundation Licensing Cloud PKI shows as active under Tenant administration > Intune add-ons, or in the license record
2 Choose the deployment model: Cloud PKI root and issuing CA, or a BYOCA issuing CA anchored to the existing private root (Chapter 04) Foundation PKI architect Decision record signed by the PKI owner
3 Plan CA count against the limit of three CAs per tenant (root, issuing and BYOCA issuing CAs all count)3 Foundation PKI architect CA plan lists no more than three CAs
4 Fix each CA’s properties before creating it: EKUs (no Any Purpose), subject, RSA key size; they can’t be edited later4 Foundation PKI architect Properties reviewed against the issuance policy
5 Cloud root model: create the Cloud PKI root CA, then the issuing CA under it, with a licensed tenant (HSM-backed keys), not during a trial (trial CAs keep software keys)5 Foundation PKI admin Both CAs show Active in Tenant administration > Cloud PKI
6 BYOCA model: create the BYOCA issuing CA and download its certificate request6 Foundation PKI admin CA status reads Signing required; .req file saved
7 BYOCA model: sign the request on the private CA with the Subordinate Certification Authority template (the program signs with the offline root); export the signed certificate and the full chain as .p7b7 Foundation PKI admin Signed .cer and chain file in the ceremony record
8 BYOCA model: upload the signed certificate and chain to the BYOCA issuing CA8 Foundation PKI admin Status Active; root common name shows External root CA
9 Record each CA’s CRL distribution point and AIA URIs from its properties. Intune hosts them for Cloud PKI CAs; for BYOCA, the parent CRL and AIA come from the private CA, and AD CS defaults to an LDAP AIA location9 Foundation PKI admin URIs listed in the CA register
10 Confirm every CRL and AIA URL is reachable over HTTP from inside the network and from the internet Foundation Network HTTP 200 from both locations; private-CA LDAP-only locations replaced
11 Download each CA certificate in DER .cer form (Cloud PKI: CA properties > Download)1011 Foundation PKI admin Files match the CA register thumbprints
12 For each CA that will issue user certificates for Entra CBA, add it to the Entra ID PKI-based trust store (checklist A.2, step 5) Foundation Identity admin CA listed in the trust store with its CRL URL
13 Create a trusted certificate profile per platform for the root, for each intermediate, and for the issuing CA; for BYOCA, one for every CA in the private chain plus the BYOCA issuing CA1213 Foundation Intune admin Profiles exist for Windows, iOS/iPadOS, Android and macOS as needed
14 Assign the trusted certificate profiles to every group that will get a cloud SCEP profile or a Wi-Fi, VPN or email profile using one14 Foundation Intune admin Assignment report
15 Confirm trusted certificate profile success on at least 99% of targeted devices Foundation Intune admin Profile device status report
16 Deploy the cloud chain to domain-joined relying parties (RADIUS, VPN, mTLS servers) by Group Policy or certutil -dspublish <file> RootCA (Chapter 07) Foundation AD admin certutil -verify on a relying party builds the chain without errors
17 Decide whether any cloud CA will issue logon certificates for the forest; publish to NTAuth (certutil -dspublish <file> NTAuthCA) only if so Foundation PKI architect Decision record; NTAuth contents match it
18 Only if AD CS still serves SCEP or PKCS to Intune: install the current Certificate Connector release on a domain-joined server that isn’t the issuing CA, isn’t a domain controller and doesn’t host the Intune Connector for Active Directory; enable automatic updates1516 Foundation Server admin Connector listed under Tenant administration > Connectors and tokens > Certificate connectors
19 Confirm connector health and version; alert on Warning or Error status17 Foundation Intune admin Status healthy; version is a supported release
20 Issue a test certificate to a test device and validate it on each relying party type Foundation PKI admin Validation record per relying party type
21 Create the pilot Wi-Fi 802.1X SCEP profile per platform, linked to the root trusted certificate profile, with the issuing CA’s SCEP URI (leave {CloudPKIFQDN} as is); EKUs present on the issuing CA; no NDES URLs mixed in18 Pilot Intune admin Profile created; no configuration errors
22 Where the certificate will be used against AD, add a SAN URI attribute with {OnPremisesSecurityIdentifier}, in a new profile, not by editing a production profile1920 Pilot Intune admin Issued certificate’s SAN contains tag:microsoft.com,2022-09-14:sid:
23 Assign the SCEP profile to the pilot device group; keep AD CS auto-enrollment on for those devices Pilot Intune admin Certificates issued; AD CS certificates still present
24 Confirm the RADIUS servers trust the cloud chain and can reach its CRL Pilot Network NPS or RADIUS log shows successful validation
25 Verify end-to-end Wi-Fi authentication with the cloud certificate Pilot Network and PKI Successful 802.1X sessions for pilot devices
26 Create and assign the VPN SCEP profile; verify VPN authentication Pilot Intune admin, network Successful VPN sessions for pilot devices
27 Extend SCEP profiles to production rings through dynamic groups Scale Intune admin Issuance success per ring
28 For each migrated ring, remove AD CS auto-enrollment for its MIGRATE templates Scale and Cutover AD admin GPO links and template permissions updated; change record
29 Confirm no unexpired AD CS certificates remain on managed endpoints for MIGRATE use cases Cutover PKI admin Inventory report shows zero
30 Retire AD CS components that served only MIGRATE workloads (NDES and connector servers no longer needed, retired issuing CAs, their enrollment service objects and auto-enrollment GPOs), following Chapter 08; archive each CA’s database and keys first Decommission PKI admin, server admin, AD admin Decommission record committed to the evidence repository

Changes from the guide’s version: the CSR steps now apply only to the BYOCA model, because a Cloud PKI root signs its own issuing CA inside Intune; CA certificates are exported DER-encoded; the cloud chain goes to domain-joined relying parties in the Foundation wave, before the pilot needs it, not in Scale; the connector is optional and must be on a current, supported release rather than “v6.2406+”; and the strong-mapping, NTAuth and three-CA-limit steps are new.

A.2 Entra CBA configuration checklist

Work through the steps in order.

Entra CBA configuration checklist
# Step Detail Verification
1 Confirm licensing CBA itself doesn’t need a premium license, but Conditional Access needs Entra ID P1, and the PKI-based trust store’s bulk .p7b upload needs P1 or P2.2122 The guide’s mention of P2 for PIM doesn’t apply to CBA. Get-MgSubscribedSku \| Where-Object { $_.ServicePlans.ServicePlanName -contains 'AAD_PREMIUM' } returns a SKU whose CapabilityStatus is Enabled (this also catches bundles such as Microsoft 365 E3 and E5)
2 Confirm the user-to-certificate write path Cloud-only users: certificateUserIds written through the admin center or Microsoft Graph. Synced users: only Entra Connect writes it, from altSecurityIdentities or sync rules (Book 03, Chapter 09).23 A test user’s certificateUserIds holds the expected value
3 Export the CA certificates Root and every intermediate and issuing CA in the user-certificate chain. certutil -dump <file>.cer shows the expected subject, validity and key usage
4 Open the network path Allow *.certauth.login.microsoftonline.com (Azure Government: *.certauth.login.microsoftonline.us) and turn off TLS inspection for it.24 A test client completes the certificate prompt through the production proxy
5 Create the PKI-based trust store and add CAs As at least Privileged Authentication Administrator: create a PKI container, add each CA (marking roots), with the base CRL URL and, if published, the delta CRL URL.25 Prefer the PKI-based store over the classic store.26 The admin center lists each CA with its CRL URLs; for automation, GET https://graph.microsoft.com/beta/directory/publicKeyInfrastructure/certificateBasedAuthConfigurations returns the PKI27
6 Verify CRL reachability and size Each CRL URL must be an internet-reachable HTTP (recommended) or HTTPS URL, downloadable in 10 seconds, within 20 MB (commercial and GCC) or 45 MB (Azure Government) for interactive sign-in. Entra ID doesn’t support OCSP.28 From an external network, Invoke-WebRequest -Uri <crl-url> -Method Head returns HTTP 200; file size within the limit
7 Require CRL validation Turn on Require CRL validation; exempt a CA only while its CRL is being fixed.29 Setting shows on; exemption list empty or dated
8 Scope CAs if several PKIs serve different users CA scoping ties a CA to one group; one group per CA, up to 30 rules.30 Scoping rules match the population plan
9 Create the pilot groups Cloud security groups, ten to twenty users covering each certificate type, platform and CA. Use separate groups for the CBA method and for staged rollout; staged rollout doesn’t support nested or dynamic groups.3132 Get-MgGroup -Filter "displayName eq 'CBA-Pilot-Users'" returns the group with members
10 Enable the CBA method for the pilot group only As at least Authentication Policy Administrator, under Entra ID > Authentication methods > Certificate-based authentication. Never All users: a user in scope is treated as MFA-capable and can’t register other methods without satisfying MFA.33 Get-MgPolicyAuthenticationMethodPolicyAuthenticationMethodConfiguration -AuthenticationMethodConfigurationId 'X509Certificate' shows state enabled and the pilot group as target
11 Configure username bindings Order is priority. Put high-affinity bindings (IssuerAndSerialNumber or SKI to certificateUserIds) first; keep at most one low-affinity binding. Priority isn’t shown in the admin center; Graph returns it.34 The guide classed Issuer + Subject as high affinity; Microsoft classes it as low.35 The certificateUserBindings in the method configuration returned by Graph list fields and priorities as intended
12 Configure authentication bindings Default single-factor; multifactor by rule for certificates protected by a PIN or biometric (for example PIV), by issuer, policy OID, or both. Issuer-and-OID rules beat OID rules, which beat issuer rules.3637 A pilot sign-in’s log shows the expected User certificate authentication level
13 Turn on password hash sync if it isn’t on For a CBA staged rollout, password sign-in for those users works only with password hash sync.38 Entra Connect shows password hash sync enabled and current
14 Enable staged rollout for certificate-based authentication As at least Hybrid Identity Administrator, under Entra ID > Entra Connect > Connect sync > Enable staged rollout for managed user sign-in. Up to 10 groups per feature; 200 users when a group is first added; later membership changes take up to 24 hours. Synced users only.39 The staged rollout page lists the pilot groups for certificate-based authentication; via Graph, Get-MgPolicyFeatureRolloutPolicy shows a policy whose feature is certificateBasedAuthentication (an evolvable enum value, returned only with the Prefer: include-unknown-enum-members header)40
15 Sign in each pilot user once Issue a Temporary Access Pass right after adding the user to staged rollout, so the first sign-in doesn’t fall back to the federation server.41 User reaches the Entra ID sign-in page, not AD FS
16 Test CBA sign-in Pilot user signs in at the My Apps portal and chooses Use a certificate or smart card.42 Sign-in log: success; Additional Details show the certificate binding used and the authentication level.43 (The guide’s token check for "amr": ["x509"] isn’t a documented test; use the sign-in log.)
17 Expand in steps Add populations as the sign-in data supports, within staged rollout’s limits; the program’s gate is below 1% CBA failure before the next step. Staged rollout isn’t for permanent coexistence; plan the domain cutover.44 Sign-in log failure rate per step
18 Require high affinity tenant-wide Only after every in-scope user’s certificateUserIds holds correct values; a premature change locks users out.45 Test users with and without high-affinity values behave as expected in a test tenant first
19 Record the federation configuration Before conversion, capture it and back up AD FS.46 Get-MgDomainFederationConfiguration -DomainId <domain> \| ConvertTo-Json \| Out-File adfs-federation-backup.json; AD FS farm backup present
20 Convert the domain to managed Start with a test domain or the smallest; rollback is re-federation with New-MgDomainFederationConfiguration.47 Update-MgDomain -DomainId <domain> -AuthenticationType "Managed", then Get-MgDomain -DomainId <domain> shows AuthenticationType Managed
21 Turn off AD FS certificate authentication For relying parties that remain on AD FS. Users are no longer sent to AD FS for certificate sign-in
22 Remove staged rollout groups After conversion. Users who signed in to Windows with a certificate stay enabled for the CBA method long enough to refresh their primary refresh token.48 No groups assigned to the certificate-based authentication feature
23 Require phishing-resistant strength in Conditional Access Use the built-in Phishing-resistant MFA strength, or a custom strength that allows CBA (single-factor, multifactor or both, optionally by issuer or policy OID) for sensitive applications, with a device compliance requirement where needed.49 Get-MgIdentityConditionalAccessPolicy shows the policy enabled and targeting the intended apps and users
24 Monitor and alert Send sign-in logs to the log workspace; alert on CBA failures (the program’s starting threshold: more than five in 15 minutes) and on CRL errors such as AADSTS500173 and AADSTS2205012.50 A test sign-in with an expired certificate raises the alert in the configured window

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