
Cyber threats are surging, making your Atlassian ecosystem security more critical than ever.
In 2025, protecting your Jira and Confluence REST APIs isn't just a best practice—it's essential for business survival.

Without strong API authentication, you risk exposing sensitive data, project information, and valuable intellectual property to unauthorized users.

This all-inclusive blog by miniOrange Atlassian experts walks you through proven security methods, explains why outdated practices put you at risk, and shows how to implement bulletproof protection using miniOrange's Enhance API Authentication app.

## Why Atlassian REST API Security Is Critical in 2025 {#why-rest-api-security-is-critical}

Securing REST APIs is vital for preventing unauthorized access to critical business data. Atlassian provides strong authentication and authorization mechanisms to safeguard these APIs.

**Key threats**: In Jira and Confluence, APIs serve as gateways to sensitive actions—updating issues, creating pages, retrieving user data, and accessing project details.

**Impact of breaches**: A security incident can lead to data theft, project compromise, system disruption, reputational damage, and significant financial and legal consequences.

According to industry reports, 92% of organizations experienced at least one API security incident in 2023, with 50% of all API traffic remaining unmonitored. The cost of ignoring API security extends far beyond immediate **data loss**.

## Essential Security Best Practices for 2025 {#essential-security-best-practices}

**Authentication methods**: Use strong authentication, like API tokens and OAuth 2.0, instead of basic authentication.

**Access controls**: Implement IP whitelisting to restrict access to trusted networks.

**Traffic management**: Apply rate limiting to prevent denial-of-service attacks.

**Encryption**: Ensure all data uses HTTPS/TLS encryption to protect against interception.

**Monitoring**: Establish all-inclusive, logging and real-time monitoring for suspicious activities.

Atlassian officially deprecated basic authentication in 2019 and strongly recommends migrating to more secure alternatives.

## Comparing REST API Authentication Methods {#comparing-auth-methods}

### Avoid Basic Authentication (Obsolete and Risky)

Basic authentication transmits credentials as easily-decoded Base64 strings with every request. This creates significant security vulnerabilities, especially without HTTPS protection.

Why it's dangerous:

- Credentials are sent in reversible encoding
- High vulnerability to credential theft
- No built-in expiration or revocation
- Deprecated by Atlassian since 2019

**When to avoid**: Production environments, public-facing APIs, or any security-sensitive application.

### API Token Authentication: Simple and Secure

API tokens replace passwords with unique, randomly generated keys that can be easily managed and revoked.

**Benefits**:

- **Easy revocation**: Instantly deactivate compromised tokens without changing user passwords
- **Script-friendly**: Perfect for automation and third-party integrations
- **Granular control**: miniOrange's app enables user-specific tokens with group-based restrictions
- **Audit capability**: Track and monitor token usage through all-inclusive logging

### OAuth 2.0: Industry Standard for Enterprise Security

OAuth 2.0 provides secure authorization through access tokens without sharing user credentials. It's the recommended method for enterprise applications requiring delegated access.

**How OAuth 2.0 works**:

1. Application requests an access token from the identity provider (Azure AD, Okta, etc.)
2. Identity provider verifies the user and issues a short-lived token
3. Application uses a token to authenticate API requests with specific permissions

**Key advantages**:

- **No credential sharing**: Users never expose passwords to third-party applications
- **Scoped access**: Tokens grant specific, limited permissions
- **Token refresh**: Short-lived tokens can be automatically renewed
- **Enterprise integration**: Works seamlessly with existing identity providers

### JWT (JSON Web Tokens): Stateless and Scalable

JWT tokens are self-contained and digitally signed, enabling efficient authentication without database lookups.

**Why JWT is powerful**:

- **Stateless operation**: Reduces server load and improves performance
- **Self-contained**: Includes all necessary information within the token
- **Tamper-proof**: Digital signatures ensure token authenticity
- **Scalable**: Ideal for distributed systems and microservices

miniOrange's Enhance API Authentication app simplifies JWT implementation while integrating advanced security features like IP restrictions and group-based restrictions.

## Advanced Security Features for Atlassian APIs {#advanced-security-features}

Modern API security requires layered protection beyond basic authentication. miniOrange's Enhance API Authentication app provides all-inclusive security for Jira and Confluence Cloud/Data Center.

### Core Security Features

**IP and Group Restrictions**: Control API access based on network location or user groups, effectively blocking unauthorized external access.

**Read-Only Permissions**: Prevent data modification by enforcing read-only access for user groups.

**Popular IDP Support**: Integrate with various identity providers (Okta, Azure AD, AWS Cognito) for centralized security management.

**Token Management**: Instantly revoke compromised tokens or disable all tokens for specific users.

**Rate Limiting**: Protect against abuse and denial-of-service attacks with customizable request limits on API Tokens.

**Audit Logging**: Maintain all-inclusive records of all API requests, including user, timestamp, and response status.

### Advanced Access Controls

**Public API Protection**: Add authentication layers to APIs that are public by default.

**Admin-Only Token Creation**: Restrict token generation to administrators, with secure email delivery to users.

## Get Started with Secure Atlassian APIs {#get-started-with-secure-atlassian-apis}

Ready to protect your Atlassian REST APIs with enterprise-grade security?

**Step 1**: Install miniOrange's Enhance API Authentication app from the [Atlassian Marketplace](https://marketplace.atlassian.com/search?query=rest%20api%20authentication%20minOrange) (free 30-day trial available).

**Step 2**: Configure your preferred authentication method—OAuth 2.0, API tokens, or JWT—using our Complete [setup guides](https://www.miniorange.com/atlassian/rest-api-authentication-documentation).

**Step 3**: Implement security policies including IP restrictions, group-based access controls, and rate limiting.

**Step 4**: Enable complete audit logging and monitoring to track API usage and detect threats.

Don't wait for a security incident to take action.

Secure your Jira and Confluence APIs today and protect your organization's most valuable digital assets with minOrange’s Enhanced API Authentication App.

## Frequently Asked Questions {#faq}

**Q: Can I still use basic authentication with Atlassian APIs in 2025?**

While basic authentication may technically work on some on-premise instances, it's strongly discouraged for production use. Atlassian deprecated this method in 2019 due to significant security risks. You should migrate to secure alternatives like OAuth 2.0 or API tokens immediately.

**Q: What's the difference between OAuth 2.0 and JWT?**

OAuth 2.0 is an authorization protocol that defines how applications get permission to access resources, while JWT is a token format for securely transmitting information. They work together—OAuth 2.0 often uses JWT as its token format to provide both secure authorization and efficient token validation.

**Q: How do I generate API tokens in Jira?**

For Jira Cloud, navigate to your profile settings and find the "API Token" section to create new tokens. Atlassian provides options like PAT tokens or application links. You can also use our plugin to authenticate using OAuth 2.0 tokens or JWTs.

**Q: How does rate limiting improve API security?**

Rate limiting controls request frequency to prevent abuse, denial-of-service attacks, and system overload. Atlassian's Data Center products include built-in rate limiting to maintain instance stability.


Protect your Atlassian Jira and Confluence data with miniOrange’s expert guide to advanced authentication and top security practices.

Secure Atlassian REST API in 2025: Your Essential Guide by miniOrange Atlassian Experts


APIs have become the backbone of modern digital systems, enabling seamless communication between applications and services. However, they’ve also become a prime target for cyberattacks.

According to TechTarget's report Securing the API Attack Surface, 92% of surveyed organizations experienced at least one API security incident in 2023.

A recent high-profile breach, attributed to compromised user credentials in a leading enterprise system, is a stark reminder of just how devastating vulnerable APIs can be. But what if securing your APIs didn’t have to be a complex, resource-intensive task?

The solution is simpler than you might think: the **Enhanced API Authentication Plugin for Jira**. This powerful tool by miniOrange helps you fortify your REST APIs with ease, covering critical security needs without any technical hurdles.

Here’s how it works and why it’s a must-have in today’s API-driven world.


### Why API Security Can’t Be Ignored {#why-api-security-cant-be-ignored}

Every REST API endpoint is a potential gateway to your system’s sensitive data. Without robust security measures, these gateways can reveal critical information, including system configurations and user details—even to unauthorized users.

For example, APIs often rely on default authentication methods, such as basic username and password setups, which are highly vulnerable to attacks like credential stuffing and brute force. This isn’t just a risk for large organizations; **50% of all API traffic is unmonitored**, leaving many endpoints exposed to attacks like injection, DDoS, and man-in-the-middle exploits.


### How miniOrange Enhanced API Security App Protects Your Data {#protects-your-data}

Our app addresses these challenges head-on, providing a comprehensive security layer for your REST APIs:
- **Authenticate Every Access Request :** Think of your API endpoints as virtual doorways to your data. Without proper locks, anyone can sneak in. The miniOrange app ensures that **only authenticated users :** gain access to your APIs. By blocking unauthorized users, it keeps your server details and sensitive data safe from prying eyes.
- **Granular Access Controls:** Not every user should have access to every piece of information. With our app, you can define **precise permissions** for user groups or individuals, ensuring that only trusted users can interact with specific APIs. This minimizes the risk of accidental data leaks or misuse.
- **Replace Outdated Credentials with Secure Tokens :** Traditional username and password setups are no match for modern threats. Our app replaces this vulnerable method with **token-based access**, which uses secure, encrypted tokens to authenticate users. This approach significantly enhances security while making API access easier to manage.
- **Control Token Generation :** To further tighten security, the app allows admins to control who can generate API tokens. Think of it as issuing secure access badges—only your most trusted team members can grant or manage API access, reducing the chances of unauthorized token creation.


### API Security: A Rising Priority in 2024 {#api-security-priority-2024}

API security is no longer optional—it’s a necessity. Here are some trends that highlight the urgency:
- **Increased API Usage :** Gartner predicts that by 2025, **APIs will account for more than 90% of web application attack surfaces**.
- **Stricter Compliance Requirements :** Regulations like GDPR and CCPA now demand higher accountability for securing API data, with penalties for non-compliance.
- **Shift to Zero Trust :** Adopting Zero Trust means prioritizing API security to protect sensitive data and applications, ensuring no entity is trusted by default.


### Why Choose miniOrange Enhanced API Security App? {#why-choose-miniorange-api-app}

The miniOrange app is designed with one goal: to simplify and strengthen your API security so you can focus on what matters most. Whether you’re dealing with sensitive customer data or critical system operations, our app ensures your APIs are locked down without requiring a steep learning curve or technical expertise.

And if your business has unique API security needs? We offer tailored solutions to meet your specific requirements, so you’re never left vulnerable.


### Secure Your APIs Today {#secure-your-api-today}

Don’t wait until a breach forces your hand. Take proactive steps to secure your REST APIs with the **Enhanced API Authentication Plugin for Jira**.

Get in touch with our team to learn more or request a personalized demo. Together, we can close the gaps in your API security—effortlessly.


Reach out to us at **support-atlassian@miniorange.atlassian.net** or raise a support ticket by [clicking here.](https://miniorange.atlassian.net/servicedesk/customer/portal/2)

Discover how to safeguard your REST APIs with ease using the miniOrange Enhanced API Authentication Plugin for Jira. Block unauthorized access, implement token-based authentication, set granular permissions, and protect sensitive data from modern cyber threats.

Jira Rest API

Secure Atlassian REST API in 2025: Your Essential Guide by miniOrange Atlassian Experts

REST API Security: How to Secure Your REST APIs Effortlessly