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Summary – With an ever-expanding attack surface and regulatory demands, it’s crucial to encrypt both your stored data (FDE, TDE, SED) and your data in transit (TLS, IPsec, VPN), while anticipating attack scenarios and rigorously managing keys via KMS/HSM with automated rotation. By combining encryption at rest and in transit in a modular, open-source, vendor-neutral approach, you implement defense in depth without sacrificing performance or legacy compatibility.
Solution: deploy an actionable framework that integrates technology selection, key governance, and process industrialization.
In an environment where the attack surface is constantly expanding and the protection of sensitive data is a regulatory requirement, establishing a comprehensive encryption strategy is essential. This includes covering both data “at rest,” stored on disks, databases, or cloud objects, and data “in transit,” which moves between applications, users, or systems.
At the heart of this approach, key management, anticipating real attack scenarios, and industrializing processes are often overlooked. This practical guide provides an actionable framework to define where and how to encrypt, choose appropriate technologies, and secure your keys to ensure robust protection without impacting performance or locking down your architecture.
Laying the Foundations: Encryption at Rest and in Transit
Encryption at rest protects your stored data against physical theft or unauthorized access on disks and cloud objects. Encryption in transit ensures the confidentiality and integrity of data as it moves between endpoints.
Understanding Encryption at Rest
Encryption at rest aims to render data unreadable when stored on hard drives, cloud volumes, or databases when not in use. It relies on mechanisms such as Full Disk Encryption (FDE), Self-Encrypting Drives (SED), or Transparent Data Encryption (TDE) for relational databases.
When the system boots or an authorized application access occurs, the appropriate key decrypts the necessary data blocks in memory. Outside of these contexts, even if the storage medium is stolen or copied without authorization, the content remains encrypted. This is a regulatory prerequisite for GDPR, HIPAA, or PCI DSS compliance.
This security layer is transparent to users and does not directly affect the user experience, though it may introduce a slight delay at startup or during backups. In a hybrid environment, verify that your FDE or TDE tools are compatible with your cloud orchestrators and deployment pipelines.
A major Swiss industrial group deployed full server and cloud backup encryption with automated key rotation via an HSM. This example demonstrates that you can combine performance and compliance without sacrificing daily backup cycles.
Exploring Encryption in Transit
Encryption in transit protects data exchanges between clients, servers, and microservices, preventing attackers from capturing or tampering with the traffic. TLS 1.2 and TLS 1.3, paired with AES or ECC/RSA, are the standard for HTTPS connections.
Within private infrastructures, IPsec and VPNs provide end-to-end security between remote sites or between containers in a private cloud. REST or GraphQL APIs must be exposed over HTTPS to protect credentials and sensitive information.
Beyond simple encryption, these protocols also ensure server—and sometimes client—authenticity. By using certificates from an internal or third-party PKI, you control the trust chain and reduce the risk of Man-in-the-Middle attacks.
A federation of Swiss public agencies implemented an IPsec VPN network interconnecting its sites, reinforced by TLS 1.3 for its business portals. This example shows how to secure both inter-institutional traffic and user access.
Complementarity and Defense-in-Depth
Neither encryption at rest nor encryption in transit is sufficient alone. They form two defense layers addressing distinct threats: physical theft or unauthorized disk copying for the former, interception and tampering of traffic for the latter.
Adopting a defense-in-depth approach reduces the attack surface and meets internal or regulatory requirements. In a modular architecture, each component storing or transmitting sensitive data becomes a protected segment.
In a hybrid model, ensure that keys and certificates are managed consistently across on-premises and cloud environments, avoiding vulnerable “white spots.” Open-source, vendor-neutral solutions help maintain this consistency.
A mid-sized Swiss pharmaceutical firm combined TDE for its database and TLS for all its microservices, demonstrating that a holistic strategy strengthens resilience and partner confidence.
When to Encrypt What: Concrete Use Cases
Each data type or storage medium requires a dedicated technology choice and configuration to maintain performance and scalability. You should encrypt disks, databases, files, backups, cloud objects, emails, and inter-system flows.
Disks and Databases
Physical disks and virtual volumes must be protected with FDE or SED. This includes on-premises servers, virtual machines, and public cloud instances when the provider doesn’t automatically manage encryption.
For relational databases, TDE encrypts data files and logs at rest. For example, SQL Server, Oracle, PostgreSQL, or MySQL Enterprise include this feature. It remains transparent to applications while enhancing security in case of media theft.
In open-source environments, you can combine LUKS on Linux or BitLocker on Windows with an external KMS to centralize key management. This modular approach avoids vendor lock-in and enables integration with your own rotation and audit processes.
A Swiss financial services SME adopted SED for its endpoint fleet and TDE for its databases, showing that you can secure the entire ecosystem without multiplying tools or complicating maintenance.
Backups and Cloud Objects
Backups—local or cloud—are a critical link and must be encrypted at rest. Modern backup solutions often include native file encryption, sometimes in a zero-trust mode, with keys held exclusively by the client.
In cloud environments, enabling provider-side encryption for object storage buckets (S3, Blob Storage, GCS) is the minimum. For greater control, you can encrypt client-side before upload, ensuring that even the provider cannot access the data.
Keys can be stored in a cloud KMS or an on-premises HSM connected via a secure VPN. Automated key rotation and regular audits ensure that any key compromise remains time-limited.
A Swiss software publisher implemented client-side encryption for its cloud backups, proving that autonomy, security, and compliance can coexist without relying solely on the provider’s shared-responsibility model.
Emails and Inter-System Flows
Emails containing sensitive data must travel through encrypted channels (SMTPS, S/MIME, or PGP). Professional email gateways can enforce strict TLS and signing mechanisms to guarantee integrity and authenticity.
Inter-application flows (APIs, file exchanges, EDI) should be encapsulated within TLS or IPsec/VPN tunnels. In a microservices ecosystem, every HTTP or gRPC call must validate certificates and limit trust to identified entities.
For emails, a relay server can enforce end-to-end encryption, decrypting only for antivirus scanning and re-encrypting before final delivery.
A Swiss logistics company deployed S/MIME for its document exchanges and VPN tunnels for its transport EDI, showing that end-to-end protection can integrate smoothly into business processes without hindering operations.
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Managing Keys and Anticipating Attacks
The encryption key is the single most critical point of failure: its theft or compromise would render the entire system vulnerable. Strengthen its management through KMS, HSM, role separation, inventory, rotation, and disaster recovery planning.
The Central Role of KMS and HSM
A Key Management Service (KMS) or a Hardware Security Module (HSM) ensures keys are never exposed in plaintext outside a secure environment. An HSM provides a tamper-resistant physical module, while a cloud KMS offers scalability and high availability.
Role separation (security administrator, key administrator, backup operator) prevents any single individual from generating, deploying, or rotating encryption keys alone. Every sensitive action must require dual control and be logged in an immutable audit trail.
A key inventory—including creation date, usage, and lifecycle—is essential. Automating the discovery of keys in databases, files, or cloud environments prevents orphaned keys and missed rotations.
Contextual governance, aligned with your security policy, balances business objectives and regulatory constraints to define criticality levels and rotation schedules: short-lived session keys, long-term data keys, dedicated backup keys, etc.
Attack Scenarios and Threat Modeling
Attacks may target physical media theft, insider threats, traffic interception, or MITM. Each scenario must be modeled to define encryption coverage and associated controls.
In the event of a server or disk theft, robust encryption at rest prevents data recovery. During network interception, TLS or IPsec blocks eavesdropping and ensures packet integrity. A comprehensive strategy anticipates both threat categories.
Hardening also involves peripheral controls: multi-factor authentication, session locking, secrets management in vaults, and anomaly detection via SIEM.
Industrializing Rotation and Audit
Automated key rotation reduces reliance on manual processes and minimizes human error. CI/CD workflows can trigger the replacement of session or backup keys on a predefined schedule.
Regular audits, coupled with compliance reports (GDPR, NLPD, HIPAA, PCI DSS), verify that each key is used within its authorized scope, that access is logged, and that rotations occur as planned.
Disaster recovery plans (DRP) must include key availability: a secondary HSM, secure key export, or chronological replication ensures backup decryption even if the primary site is unavailable.
In hybrid infrastructures, audits must cover both on-premises and cloud. Open-source inventory and compliance tools facilitate integration and avoid vendor lock-in.
Trade-Offs and Shared Responsibilities
Encryption impacts performance, maintenance, and compatibility with legacy systems. In the cloud, shared responsibility requires clear definitions of who does what to avoid gaps.
Performance and Legacy Constraints
FDE or TDE can introduce CPU overhead and slight I/O latency increases. On high-frequency or mission-critical systems, test the impact before deployment and consider optimizing caching or upgrading CPUs.
Legacy systems, sometimes incompatible with modern HSMs or newer algorithms (ECC), may require encryption gateways or TLS proxies for a phased transition without service interruption.
An open-source–friendly hybrid strategy can deploy NGINX or HAProxy proxies to handle TLS at the edge, while gradually updating backend components, avoiding a risky “big bang” migration.
A Basel research institution built an open-source TLS proxy in front of its legacy systems, demonstrating that you can secure sensitive flows without immediately replacing the entire application stack.
Certificate Management and Renewal Cycles
TLS, PKI, and code-signing certificates have short lifecycles (often 90 days to one year). Automating issuance and renewal with ACME or internal tools prevents unexpected expirations and service disruptions.
Centralizing certificates in a single repository allows you to map dependencies, receive expiration alerts, and get a unified view of encryption and signing standards in use.
Without such tools, teams risk losing traceability and leaving expired certificates in production, opening the door to MITM attacks or connection refusals by browsers and client APIs.
A Swiss university implemented an internal ACME pipeline coupled with a centralized catalog, proving that an automated PKI reduces certificate-related incidents and improves visibility.
Shared Responsibility in the Cloud
In a public cloud, the provider often encrypts disks and network layers. However, responsibility for encrypting application data, backups, and transfers remains with the customer. Clearly document this boundary.
Provider-managed keys may suffice in some cases, but for independence and strict requirements, use a client-side KMS or a dedicated HSM.
Modeling shared responsibility also involves identity security (IAM), certificate orchestration, and VPC/VLAN configurations to ensure no unintended traffic remains exposed.
A Swiss energy company formalized its cloud responsibility matrix, validated by its CISO and external auditor, demonstrating that clear governance reduces blind spots and strengthens resilience.
Ensure Your Data Protection Today
Implementing a complete encryption strategy—covering data at rest and in transit—requires careful technology selection, rigorous key management, and process industrialization. By combining FDE, TDE, TLS, VPN, KMS, HSM, automated rotation, audits, and PKI, you create an environment resilient to internal and external attacks.
Every project is unique and demands a contextual, modular, and scalable approach that favors open-source solutions and avoids vendor lock-in. Our experts can help you define, implement, and maintain an encryption architecture tailored to your business needs and regulatory obligations.
