To secure SaaS applications, protect sign-ins, limit access, review each service’s security settings, and make sure you can detect and recover from incidents. Security is shared: providers operate the service and its underlying infrastructure, while customers usually control important choices such as user access, authentication, data sharing, and logging. The exact division—and the controls available—varies by product, so verify it in the provider’s documentation and agreement.
Use this checklist as a starting point for a small or midsize organization. Prioritize controls according to the sensitivity of your data and the importance of each workflow; contractual and regulatory requirements may call for additional safeguards.
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1. Inventory your SaaS applications and critical data
You cannot protect services you do not know the organization uses. Build and maintain an inventory of business SaaS tools, their owners, the data they hold, and the workflows that depend on them. Include services adopted by individual teams, not only those purchased centrally.
For each service, record who administers it, how users sign in, what information is stored or shared, and where to find the provider’s security and recovery documentation. Identify the applications whose loss or compromise would most disrupt operations; those should receive the earliest and most frequent attention.
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2. Require MFA, especially for administrators
Require multifactor authentication (MFA) for business SaaS accounts wherever the service supports it. Start with administrators and accounts that handle sensitive information, then extend the requirement to all users. CISA advises organizations to aim for phishing-resistant MFA in its MFA guidance.
Where supported by both the SaaS service and your identity provider, a FIDO2-compatible security key is a strong choice: CISA ranks security keys above app codes and text or email codes for protection against phishing. CISA also describes authenticator-app number matching as a stronger option than app one-time codes, with biometrics best used alongside another factor. Compatibility depends on the service’s protocols, devices, operating systems, ports or NFC, and account-recovery process; confirm those details before buying keys or enforcing a method. Avoid relying on text or email codes when a stronger supported option is practical.
Keep account recovery in scope: define who can reset MFA, how a lost device is handled, and how to prevent a recovery process from bypassing the protection you just enabled.
3. Grant only the access each role needs
Use least privilege: give users only the permissions required for their work. Keep routine accounts separate from administrative accounts where the product allows it, and restrict powerful roles to the smallest practical number of people. Apply the same scrutiny to integrations, service accounts, contractors, and other third parties. CISA’s #StopRansomware Guide and NIST’s EO-Critical Software FAQs provide supporting access-control guidance; the NIST material has a specific federal executive-order context and is not a universal legal requirement for businesses.
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Review role assignments periodically and whenever a person’s responsibilities change. Remove dormant accounts and revoke access promptly when someone leaves. For external users and vendors, confirm that access is still needed, narrowly scoped, and has an owner and end date where appropriate.
4. Review each service’s security configuration
Do not assume the provider’s default settings match your needs. Use the product’s administrative controls to review sign-in requirements, password and session settings, sharing permissions, administrator roles, integrations, and audit options. Make the review repeatable: assign an owner, document the intended settings, and revisit them after significant product or organizational changes.
CISA’s Small and Medium-Sized Business Resources page points to SCuBA, a free resource for assessing and hardening SaaS configurations. Use it where its coverage applies, and check the current tool guidance and product support before relying on it for a particular service. A checklist or assessment tool does not replace reviewing the settings and responsibilities specific to your provider.
5. Protect credentials, tokens, and secrets
Treat passwords, API keys, access tokens, recovery codes, and integration secrets as credentials. Store them only in approved, access-controlled systems; do not put them in shared documents, tickets, source code, or chat messages. Limit who can create or retrieve them, use expiration or rotation options where available, and revoke them when an integration or user no longer needs access.
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Review connected apps and integrations as part of access reviews. An integration can retain meaningful access even after a person changes roles, so identify its owner and the data and actions it can reach. Restrict administrative privileges and avoid using high-privilege credentials for routine tasks.
6. Enable audit logs and check what they contain
Turn on the activity and audit logs each service makes available. Check whether they record the events you would need to investigate, such as sign-ins, file or record sharing, administrative changes, permission updates, and changes to logging itself. Features, event detail, export methods, and retention vary by provider; verify the specifics in the service documentation and agreement.
Compare the available retention period and event detail with your likely investigation needs. If the service does not provide the coverage or retention you require, document the gap and consider whether another control or product is needed. CISA’s logging guidance and NIST SP 800-171 Rev. 3 offer useful control examples; SP 800-171 is specifically for protecting controlled unclassified information (CUI) in nonfederal systems, not a blanket requirement for every SaaS customer.
7. Centralize logs and alert on suspicious activity
When practical, export SaaS logs to a central place your organization monitors. Centralization makes it easier to review activity across services and helps preserve evidence if a SaaS administrator account is compromised. Restrict who can access, change, or delete collected logs.
Set alerts for events that matter to your risk, such as unusual sign-ins, privilege changes, and attempts to disable or alter logging. Assign someone to receive and act on alerts; an alert with no response owner is not an effective detection process. CISA’s Cloud Security Technical Reference Architecture discusses cloud logging and monitoring in a government architecture context; use it as a control reference rather than a universal mandate.
8. Know how SaaS data and configuration can be recovered
Find out what the provider can restore, what you must preserve yourself, how long data is retained, and whether configuration can be recovered as well as content. Do not assume that a SaaS subscription includes a customer-controlled backup or the same recovery window as another service. Check where any separate backup is held, who can access it, and whether it is protected from compromise of the primary tenant.
Test restoration of representative data and, where possible, configuration. Confirm who is authorized to restore, how long the process takes, and whether the restored information is usable. CISA’s cloud architecture and NIST’s EO-critical software guidance discuss recovery-related controls, but the operational and contractual boundary is product-specific; confirm it with the provider.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.9. Prepare a SaaS-aware incident response plan
Include SaaS incidents in your response plan rather than treating them as ordinary device outages. Define who can decide to disable accounts or integrations, who contacts the provider, who preserves evidence, and who communicates with employees, customers, or other affected parties. Keep provider support and security escalation paths accessible even if your usual account or email service is unavailable.
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Write down how your team will report a suspected compromised account, request provider assistance, preserve available logs, and coordinate containment and recovery. Exercise the plan with a realistic scenario, such as an administrator account takeover or unauthorized sharing of sensitive files. NIST SP 800-61 Rev. 3, published in April 2025, is a broader incident-response reference associated with CSF 2.0: NIST SP 800-61 Rev. 3. It is guidance, not a substitute for your service-specific procedures.
10. Recheck controls when services or risks change
Make SaaS security a recurring task, not a one-time setup. Revisit the inventory, access, configuration, logging, recovery, and response arrangements on a schedule that reflects the service’s importance and data sensitivity. Trigger an additional review when you adopt a new service, enable a major integration, change identity or sharing settings, or experience a security incident.
For each application, keep a short record of the owner, critical data, enabled safeguards, known limitations, provider contacts, and next review date. This helps a small team focus effort where it matters and makes gaps visible before an incident.
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