How to Lock Down S3 Access With VPC Endpoints and Evidence You Can Prove

S3 sits at the center of most environments, handling backups, logs, and data pipelines. Leaving that traffic on public routes adds both exposure and cost. Using an S3 VPC endpoint keeps traffic private inside AWS, adds control through endpoint policies, and simplifies how workloads connect to data.

This guide takes AWS’s framework and transforms it into something you can actually run: an operational playbook built around governance, verification, and proof.

Methods to secure and prove private S3 access with VPC endpoints

Before starting, prepare the following to support configuration, validation, and evidence collection.

📌 General prerequisites:

• An inventory of Virtual Private Clouds (VPCs), subnets, route tables, and S3 buckets for each tenant.
• Identity & Access Management (IAM) roles and a baseline S3 bucket policy model.
• Permissions to create and manage VPC endpoints and to view CloudTrail and VPC Flow Logs.
• A staging account or VPC where you can safely test configuration changes.
• A workspace or repository for storing monthly evidence packets.

Step 1: Confirm your S3 endpoint strategy

Before locking down S3 access, define how workloads reach it privately through VPC endpoints. In this step, you confirm whether each uses a Gateway Endpoint (standard for S3 and DynamoDB) or an Interface Endpoint (PrivateLink), as the choice impacts cost, performance, and security.

Steps:

1. First, review the available endpoint options and understand the differences between Gateway and Interface endpoints. Use the table below to help guide your selection.

💡 S3 also supports Interface endpoints, but they are rarely necessary except for advanced DNS or network-isolation use cases.

2. Document the selected endpoint type for each VPC along with its supporting details, including Region, routing method (route table or Private DNS), Availability Zone coverage, cost model, and business or compliance rationale.
3. Record the owner responsible for managing each endpoint and define a review schedule to ensure that configurations remain accurate over time.
4. Turn on S3 Block Public Access at both the account and bucket levels before applying endpoint restrictions to guarantee that no public access paths exist.

Step 2: Design routing and DNS behavior

After selecting your endpoint strategy, configure routing so all S3 traffic flows through the VPC endpoint instead of the public internet. This includes updating route tables, validating DNS resolution, and documenting the network path for each tenant or environment.

Steps:

1. Associate the AWS VPC S3 Gateway Endpoint with the route tables used by the subnets that require access to S3. AWS automatically manages the S3 prefix-list (pl-xxxx) routes in those tables once the association is complete.
2. Enable Private DNS for Interface endpoints so that service names resolve to the private IP addresses of the endpoint ENIs. For Gateway endpoints, DNS resolution remains unchanged, but routing ensures that traffic stays within the AWS network and does not traverse the internet.
3. Verify that S3 traffic doesn’t rely on default routes (0.0.0.0/0) that would send requests through a NAT gateway or internet gateway, and that the S3 prefix-list routes take precedence.
4. Create a brief diagram for each VPC or tenant that shows how packets are routed from the workload to the S3 endpoint. Include a short paragraph summarizing the data path, specifying which subnets and routes are used.

💡 Tip: Use tools such as VPC Flow Logs, Reachability Analyzer, or CloudTrail to confirm that S3 traffic is routed through the endpoint and not over the public internet.

Step 3: Author least privilege endpoint policies

Next, define what traffic can pass through the VPC endpoint. Least-privilege endpoint policies limit which S3 actions and resources can be accessed through the endpoint, providing a traffic-level control that complements IAM and bucket permissions.

Steps:

1. Identify the specific S3 buckets, prefixes, and actions required by the workloads using the endpoint.
2. Write a JSON policy that allows only the necessary actions on the defined resources. For example:

3. Record the purpose of the policy in your configuration documentation or Infrastructure-as-Code repository. Include the workload name and reason for the access pattern.
4. Link the endpoint policy to the corresponding bucket policy to maintain consistent access control.
5. Store approved endpoint policies in a shared repository for future reuse across tenants or environments.

Step 4: Align bucket policies with endpoint controls

To fully lock down AWS S3 bucket private access, configure each bucket to accept traffic only through approved endpoints. This step links network control (the endpoint) and resource control (the bucket) to form a closed, private access boundary.

Steps:

1. Create a base bucket policy that denies all S3 actions unless the request meets specific allow conditions.
2. Add a condition that allows access only through approved endpoint IDs.

📌 Note: The aws:SourceVpce condition restricts access to specific VPC endpoint. In multi-account, cross-VPC, or service-integrated scenarios (such as access via AWS services), additional conditions may be required to avoid unintended access blocks or gaps.

3. Add a condition that denies unencrypted traffic.

📌 Note: This TLS condition is evaluated by Amazon S3 on the request itself and applies regardless of whether access occurs through a VPC endpoint.

4. If multiple accounts are in use, restrict access to your organization or specific account IDs.

📌 Note: The aws:PrincipalOrgID condition applies only when AWS Organizations is in use. It doesn’t replace endpoint restrictions or IAM-based access controls and should be used as an additional scoping condition.

5. Store the final bucket policy alongside the endpoint policy in your evidence repository or Infrastructure-as-Code files.
6. Run S3 Access Analyzer to detect any unintended access paths.
7. Keep resources at a minimal level and rely on explicit deny statements for enforcement.

Step 5: Validate end-to-end in staging

Before deploying to production, test your endpoint strategy, routing, and access controls in a staging environment. Testing in a staging environment helps confirm that when you configure S3 VPC endpoints, traffic flows privately and no fallback routes exist.

Steps:

1. Deploy an EC2 instance in a subnet that has a route to the S3 Gateway Endpoint and perform GetObject and PutObject operations on a test bucket using the AWS CLI or SDK.
2. Launch another EC2 instance in a subnet without the S3 endpoint route, using the same IAM role and permissions as the first instance, and attempt the same operations. These requests should fail, confirming that access is enforced by routing and endpoint configuration rather than IAM authorization.
3. Capture the results. Record:
   • Route table snapshots showing endpoint routing.
   • CLI output or SDK logs from both instances.
   • CloudTrail data events showing successful and denied S3 API calls, including the vpcEndpointId.
   • VPC Flow Logs providing supporting network-level context for traffic paths (for example, confirming traffic stays within approved subnets and doesn’t traverse NAT or internet gateways).
4. Write a summary describing the test environment, results, and confirmation that S3 access is private and enforced.

Step 6: Prove private access with logs and traces

After confirming functionality in staging, collect evidence that all S3 traffic flows through approved VPC endpoints. Use VPC Flow Logs and CloudTrail data events to verify that every request follows the intended private path.

Steps:

1. Enable VPC Flow Logs for the subnets that host workloads accessing S3 and send the logs to CloudWatch or S3 for analysis.
2. Use Athena or CloudWatch Logs Insights to query Flow Logs for traffic to S3 IP ranges or the endpoint ENIs. Confirm that traffic originates from approved subnets.
3. Query CloudTrail for PutObject, GetObject, and other S3 API calls. Check that the events include the correct vpcEndpointId, IAM principal, and expected source context.

📌 Note: The vpcEndpointId field is present in CloudTrail S3 data events and shouldn’t be expected in VPC Flow Logs.

4. For Interface endpoints, validate that traffic targets the endpoint ENIs by reviewing VPC Flow Logs and confirming destination IPs map to the endpoint network interfaces.

For Gateway endpoints, validate that S3 requests are routed via the S3 prefix-list and do not traverse NAT gateways or internet gateways, and confirm the vpcEndpointId in CloudTrail S3 data events.

5. Save query results, log samples, and screenshots showing S3 requests with the correct vpcEndpointId, evidence that traffic doesn’t traverse NAT gateways or internet gateways, and both successful and denied attempts.
6. Store the evidence with your monthly compliance documentation for audit reference.

Step 7: Integrate with dependent services

Once S3 access is restricted to private endpoints, validate that workloads and dependent services continue to operate correctly. Confirm that applications, pipelines, and batch jobs use the private path and follow the enforced access controls.

Steps:

1. List all workloads that interact with S3, including analytics jobs, ETL pipelines, and serverless functions.
2. Review IAM roles for each service and confirm that permissions align with endpoint and bucket policies. Avoid wildcard actions and resources.
3. Deploy or run each service from subnets connected to the S3 Gateway endpoint. If you are using an Interface endpoint, also verify Private DNS configuration and Security Group rules to ensure traffic resolves to and is permitted through the endpoint ENIs.

💡 See the AWS Neptune bulk load guide for VPC setups for a practical example.

4. Test access by performing read and write operations from each workload and review the available logs to confirm that requests follow the intended private access path, using CloudTrail S3 data events as the primary validation source where applicable.
5. Measure performance metrics before and after the change to confirm consistent throughput and stability.
6. Create a simple integration checklist that records IAM validation, routing, job results, and log verification for future reference.

Step 8: Operate change control and exceptions

After enforcing private S3 access, maintain it through structured change management and regular exception reviews. Each modification or temporary policy change should have a defined purpose, accountable owner, and expiration date.

Steps:

1. Treat every endpoint or bucket policy update as a formal change. Record the purpose, potential impact, rollback plan, validation steps, change owner, and reviewer.
2. Document temporary exceptions that expand access. Include the reason for the exception, the compensating controls in place, and an expiry date for review or removal.
3. Keep a list of all open exceptions and review it weekly to confirm whether they are still required, have expired, or are ready to be closed.
4. Archive all policy and endpoint changes by saving change tickets, policy diffs, and rollback confirmations in your evidence repository.
5. Review recurring exceptions and determine whether a design or process update is needed to eliminate repeated temporary access.

Step 9: Publish a monthly evidence packet

The final step in locking down and proving private S3 access is to package your evidence into a consistent monthly report. This packet provides a complete view of endpoint configurations, policy changes, and access validation across all tenants.

Steps:

1. List all VPC endpoints per tenant, including the endpoint IDs, associated VPCs, service types, owners, and review dates.
2. Attach the current endpoint and bucket policies. Highlight differences from the previous month to show changes or policy tightening.
3. Export route table configurations that direct S3 traffic through the Gateway endpoint and include subnet associations and route targets.
4. Add CloudTrail samples for PutObject, GetObject, and other S3 API calls that show the expected principals, source VPCs, and the correct vpcEndpointId.
5. Include filtered VPC Flow Logs or Athena query results proving that traffic originated from approved subnets and passed through private endpoints.
6. Append exception logs from Method 8 and note which entries were reviewed, extended, or closed.
7. Write a summary describing the month’s key changes, test outcomes, and any incidents or exceptions.

💡 Use a consistent layout and naming format each month and store packets in a version-controlled repository or dashboard organized by tenant.

Best practices summary table

Use this table as a quick reference for the core practices in securing S3 with VPC endpoints. It highlights what each practice achieves and the value it delivers.

Automation touchpoint example

To maintain control and visibility over private S3 access, automation can help enforce consistency and catch drift. Here’s a sample workflow:

• A nightly job lists all VPC endpoints and their associated route tables, then pulls the current endpoint and bucket policies for comparison against approved baselines.
• A scheduled query extracts relevant CloudTrail S3 events and VPC Flow Log samples tied to those endpoints to verify actual usage.
• Each month, a task compiles a PDF packet containing configuration diffs, validation proofs, and exception aging, then stores it in the designated documentation workspace.

NinjaOne integration

NinjaOne can help automate evidence collection and documentation for private S3 access. Here’s how it can support ongoing validation and reporting tasks:

Sustaining secure and verified operations through S3 VPC endpoints

Securing S3 access doesn’t have to slow you down. Choose the right endpoint, connect it to your buckets, and keep the evidence flowing. When you manage it like any other system control with clear ownership, regular checks, and a traceable record, you build trust that lasts well beyond the configuration itself.

Related topics:

• What is AWS CloudTrail? Definition & Overview
• The Real Benefits of Cloud Services
• Data Protection Plan: Guide & 8 Steps for Creation
• Taking Control in the Endpoint Era