ClickHouse on sovereign clouds: compliance-aware analytics reference

Hook: Why regulated teams can't treat analytics like a public cloud afterthought

If you run analytics for a regulated business in the EU — finance, health, telco, public sector — your biggest risks are not slow queries but where data lives and how it moves. Cross-border transfers, weak key management, and backups that replicate outside EU jurisdiction break compliance contracts and expose you to fines and audit findings. In 2026 the landscape changed: hyperscalers added EU sovereign offerings, and ClickHouse’s rapid product momentum made it a realistic, high-performance analytics engine for regulated workloads. This guide shows how to deploy ClickHouse in EU sovereign clouds with compliance-first data residency, encryption, and backup strategies that auditors will understand.

Executive summary — the bottom line up front

Deploy ClickHouse into an EU sovereign cloud using a few non-negotiable controls: region-locked compute and storage, provider or self-managed KMS with envelope encryption, audit-ready backup workflows, and network and policy controls to prevent accidental egress. For Kubernetes: use a ClickHouse Operator with CSI storage classes scoped to EU-only object storage endpoints and a Secrets/Keys flow that separates operator credentials from KMS access. For VMs: run ClickHouse replicas across AZs within the sovereign region and use the provider’s encrypted block storage + S3-compatible EU-only endpoints for backups. This article provides reference architectures, security patterns, migration steps, and reproducible config snippets.

Why 2026 is a turning point for sovereign analytics

Late 2025 and early 2026 brought two trends that matter for regulated analytics teams. First, major cloud vendors launched dedicated sovereign regions and assurances (for example, the AWS European Sovereign Cloud announced in January 2026). Second, ClickHouse continued rapid enterprise adoption (notably the $400M funding momentum in 2025), making it a favored OLAP engine for low-latency analytics. Combining an EU sovereign cloud with ClickHouse gives you the performance and compliance assurances required by customer contracts and national regulations.

Core design priorities for ClickHouse in EU sovereign clouds

• Data residency by design — all persisted data (local parts, object storage, and backups) must remain within EU sovereign region boundaries.
• Encryption in motion and at rest — TLS for all client and inter-node traffic; provider-managed or self-hosted KMS with envelope encryption for object backups.
• Authorized key management — no static keys in application configs; use IAM roles, short-lived credentials, or Vault-like services.
• Backup retention and immutable snapshots — tamper-evident backups, versioning, and retention policies aligned with compliance needs.
• Operational observability and auditability — logs, access traces, and documented runbooks for DR and data access requests.

Reference architectures

1) Kubernetes-managed ClickHouse (recommended for cloud-native teams)

Use a ClickHouse Operator (such as Altinity/ClickHouse operator or upstream operator) running on a Kubernetes cluster provisioned inside the EU sovereign region. Storage uses CSI-provisioned PVCs attached to each ClickHouse pod and S3-compatible object storage endpoints restricted to the EU region for backups.

Key components:

• Kubernetes cluster in EU sovereign region (control plane and nodes restricted to EU).
• ClickHouse Operator for lifecycle and schema management.
• ClickHouseKeeper (or ZooKeeper if you prefer) in-region for metadata/coordination.
• Provider-managed block storage with volume encryption for data parts.
• S3-compatible object storage endpoint in the same sovereign region for backups.
• HashiCorp Vault or cloud KMS in-region for envelope key management.

2) VM-based ClickHouse (recommended for teams that need control over kernel/tuning)

Deploy ClickHouse on VM instances inside the sovereign region. Use managed block storage encrypted with customer-managed keys and a dedicated in-region object storage endpoint for backups. Replicate across availability zones inside the EU region for HA.

Key components:

• VM fleet inside EU sovereign region.
• ClickHouse clusters with shard + replica topology inside the region.
• In-region ClickHouseKeeper ensemble for coordination.
• Provider KMS for DEKs, with manifests referencing KMS ARNs but never storing plaintext keys on disks.

Data residency controls — practical checklist

1. Pin compute and storage to an EU sovereign region and document region IDs used for every resource.
2. Restrict bucket/object replication: disable cross-region replication and block public bucket replication settings.
3. Use network controls (VPC endpoints, private endpoints) so backups and client traffic never traverse public internet paths that exit the region.
4. Enforce domain allowlists for external integrations (e.g., analytics dashboards, ETL workers) so third-party services that are not EU-resident cannot access sensitive data.
5. Maintain an inventory mapping ClickHouse databases/tables to residency classification used in contracts and audits.

Encryption and key management patterns (with examples)

The safest pattern is envelope encryption: generate a Data Encryption Key (DEK) per backup or per object, encrypt data client-side or via server-side mechanisms, and encrypt DEKs with a Key Encryption Key (KEK) stored in a KMS/Vault. This avoids exposing plaintext DEKs in object storage and gives auditors a clear key lifecycle.

Example: Envelope encryption for ClickHouse backups using AWS KMS (EU sovereign)

# Encrypt file using AWS KMS (replace KEY_ID/EU_ENDPOINT placeholders)
aws --endpoint-url https://kms.eu-sovereign.example kms encrypt \
  --key-id arn:aws:kms:eu-sovereign-1:123456789012:key/KEY_ID \
  --plaintext fileb://path/to/backup.sql \
  --output text --query CiphertextBlob | base64 --decode > backup.sql.encrypted

# Upload to S3-compatible endpoint in EU sovereign region
aws --endpoint-url https://s3.eu-sovereign.example s3 cp backup.sql.encrypted s3://clickhouse-backups/2026-01-XX/

For Kubernetes, prefer using a SecretsOperator that fetches DEKs from Vault and performs encryption in a short-lived pod. Avoid storing DEKs in Kubernetes Secrets unless they are sealed/encrypted with a tool such as Mozilla SOPS (backed by KMS or Vault).

TLS and inter-node encryption

• Enable TLS for client-server and inter-server communication in ClickHouse config. Use certificates issued by an internal CA or a private PKI inside the sovereign region.
• Rotate node certificates regularly and automate rotation using cert-manager on Kubernetes or a VM-based automation tool.

Backup strategies that pass audits

Backups are your primary proof during an incident. Auditors will ask: are backups stored in-scope, encrypted, and immutable? Implement a layered backup strategy:

1. Continuous replication: Replication within the region for HA (ClickHouse replicas and shards) so node failures do not require restore.
2. Scheduled physical backups: Use clickhouse-backup or custom scripts to create physical snapshots of parts and upload to EU-only object storage with server- or client-side encryption and versioning enabled.
3. Immutable storage/retention rules: Use object lock (WORM) or immutable buckets where supported for required retention windows.
4. Tested restores: Schedule restore drills quarterly and keep logs/traces of tests to demonstrate recoverability.
5. Offsite but in-region copies: Keep copies in multiple sovereign zones within the EU region (not cross-border), to survive AZ and provider-level incidents if the provider supports multi-AZ within the sovereign jurisdiction. Consider micro-DC / PDU planning to support on-prem resilience: see micro-DC PDU & UPS orchestration playbooks for hybrid bursts.

Sample Kubernetes CronJob for encrypted backups

apiVersion: batch/v1
kind: CronJob
metadata:
  name: clickhouse-encrypted-backup
spec:
  schedule: "0 2 * * *" # nightly
  jobTemplate:
    spec:
      template:
        spec:
          serviceAccountName: clickhouse-backup-sa
          containers:
          - name: backup
            image: myorg/clickhouse-backup:latest
            env:
            - name: S3_ENDPOINT
              value: "https://s3.eu-sovereign.example"
            - name: KMS_ENDPOINT
              value: "https://kms.eu-sovereign.example"
            command: ["/bin/sh", "-c"]
            args:
            - |
              /usr/local/bin/clickhouse-backup create --config /etc/clickhouse-backup/config.yml nightly
              /usr/local/bin/encrypt-with-kms --kms-endpoint $KMS_ENDPOINT --key-id key-arn --input /backups/nightly.tar.gz --output /backups/nightly.tar.gz.enc
              /usr/local/bin/s3put --endpoint $S3_ENDPOINT /backups/nightly.tar.gz.enc s3://clickhouse-backups/$(date +%F)/
          restartPolicy: OnFailure

Migration guide — from public region or on-prem to EU sovereign ClickHouse

Migrating analytics data is risky if you break residency guarantees. Use staged migration with dual-write, backfill, and verification phases. Below is a high-level playbook — for a full migration plan, see How to Build a Migration Plan to an EU Sovereign Cloud Without Breaking Compliance.

Phase 0 — assessment and planning

• Inventory data: classify tables by sensitivity and residency requirements.
• Decide the topology: shards, replicas, and resource sizing (CPU, memory, disk I/O).
• Pick storage endpoints: in-region block storage, object storage endpoints, and KMS/Vault.

Phase 1 — build target infrastructure

1. Create the sovereign cluster (K8s or VM nodes) in the EU region and harden network policies.
2. Deploy ClickHouse cluster with operator and ensure Keeper ensemble is in-region.
3. Configure TLS, KMS access, and backup buckets with encryption and immutability rules.

Phase 2 — sync and validate

• For large tables, use ClickHouse replication and clickhouse-copier to copy data from source cluster to target. This preserves parts and minimizes downtime.
• Run parallel validation queries comparing aggregated outputs (row counts, checksums) between source and target.
• Monitor performance characteristics: merge rates, disk pressure, and memory usage on the target.

Phase 3 — cutover

1. Switch analytic clients to the new cluster progressively: start with reporting jobs, then BI dashboards, then real-time consumers.
2. Maintain dual-write if you require a rollback path, and schedule a final sync of delta data before fully decommissioning the old resource.
3. Create an audit package (configuration, access lists, key policies, backup manifests) for the compliance team.

Operational best practices — maintain compliance at scale

• Least privilege IAM: grant only needed permissions to backup services and operator controllers.
• Secrets lifecycle: rotate service keys quarterly and keep rotation documented.
• Monitoring and alerting: instrument ClickHouse metrics (merge failures, replication lag) and backup pipeline health.
• DR runbooks: maintain runbooks that map a compliance incident to the technical recovery steps and to communications templates for regulators. See micro-DC guidance for hybrid resilience here.
• Periodic audits: run quarterly checks to ensure no S3 buckets or compute nodes are accidentally configured outside the sovereign region.

Case study (anonymized): EU payment processor moves ClickHouse to a sovereign cloud

Background: a European payments company owned sensitive transaction metadata and was under contractual obligations to keep data inside the EU. They needed low-latency analytics for fraud detection and reporting. Their challenges were cross-border backups in their existing multi-cloud setup and unmanaged keys in application configs.

What we implemented:

• Provisioned a Kubernetes cluster in an EU sovereign cloud region, with control-plane access limited to EU-based admin accounts.
• Deployed a ClickHouse cluster using an operator and configured ClickHouseKeeper for coordination inside the region.
• Implemented envelope encryption for backups: a per-backup DEK encrypted with a KEK in an in-region KMS; backups uploaded to an S3 endpoint locked to the EU region with object lock enabled for retention.
• Automated certificate rotation with cert-manager and used Vault for temporary credentials for backup jobs.

Results: the company met their contractual residency requirements, reduced risk of cross-border transfer, and gained a tested restore procedure that satisfied auditors. Performance of analytic queries improved due to localizing data and optimizing shard layouts for their workload.

Advanced strategies & future-proofing (2026 and beyond)

As sovereign cloud offerings mature, expect richer compliance attestations and new features such as immutable managed backup tiers and in-region confidential computing. Plan for:

• Confidential VMs and TEEs — for workloads requiring hardware-backed isolation.
• Policy-as-code for residency — automate region guards using OPA/Gatekeeper to prevent resource creation outside sanctioned regions.
• Federated query patterns — keep sensitive datasets in-region while exposing aggregated results via controlled APIs for global consumers.
• Consider edge caching and locality strategies for cross-service performance in hybrid scenarios.

Quick checklist — minimum viable compliance for ClickHouse in EU sovereign clouds

• Compute and storage provisioned only in the chosen EU sovereign region(s).
• Backups uploaded to EU-only object storage endpoints with versioning and immutability where required.
• All backups encrypted; DEKs protected by an in-region KMS/Vault and rotated on schedule.
• Inter-node and client-server TLS enforced with in-region PKI.
• Regular restore drills and audit logs retained per retention policy.

Common pitfalls and how to avoid them

• Pitfall: Using a globally-scoped bucket name that triggers provider replication. Fix: Use region-specific buckets and explicitly disable replication and cross-region copy jobs.
• Pitfall: Putting KMS keys in app config. Fix: Use short-lived credentials or Vault; never persist KEKs/DEKs on disk in plaintext.
• Pitfall: Backups transferred via public internet to a non-EU staging endpoint. Fix: Create private VPC/S3 endpoints and enforce routing rules to keep traffic inside-region.

Tools & open-source projects to include in your stack

• ClickHouse Operator (k8s) — cluster lifecycle and schema management.
• clickhouse-backup — de-facto tool for physical backup/restore workflows. (See practical pipeline notes in migration guides.)
• HashiCorp Vault — key management and short-lived credential generation.
• Cert-manager — automate TLS issuance and rotation inside Kubernetes.
• OPA/Gatekeeper — enforce region policies for resource creation.

"In 2026, winning at regulated analytics means pairing high-performance engines like ClickHouse with sovereign cloud contracts and airtight operational controls." — Practical takeaway from enterprise migrations

Final checklist before you go live

1. Confirm all storage endpoints (block & object) are in EU sovereign regions and replication is disabled.
2. Verify encryption: TLS enabled for all channels and backups encrypted with keys in an in-region KMS/Vault.
3. Document key access workflows so auditors can trace who can decrypt backups.
4. Run a full restore test to a clean environment and validate analytics queries used in production reports.
5. Schedule periodic compliance reviews and DR drills (quarterly recommended).

Call to action

Ready to move ClickHouse into an EU sovereign cloud without compromising compliance? Start with a 2-week audit and a 6-week migration sprint: inventory your datasets, stand up a scoped sovereign cluster, and run an end-to-end backup-and-restore drill. If you want a starter kit, download our reference Helm charts, encrypted-backup scripts, and an audit checklist tuned for EU sovereign deployments.

Contact us to get the kit and a tailored migration plan for your ClickHouse workloads — we’ll help you choose the right topology, secure keys correctly, and prove recoverability to your auditors.

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