Common Problems IT Leaders Face with Java EE Application Servers

For many IT leaders and enterprise architects, managing a Java EE application server is a critical part of ensuring smooth operations, security, and scalability. However, as technology advances and business demands evolve, many organizations find themselves struggling with outdated or inefficient servers that create more problems than they solve.

If you’ve ever faced unexpected downtime, integration headaches, or rising maintenance costs, you’re not alone. Below are some common challenges IT leaders encounter with Java EE servers—and why these issues might be a sign that it’s time to reconsider your current setup.

---

1. Performance Bottlenecks & Scalability Challenges

• The Problem:
  • As business applications grow, servers often struggle to handle increased traffic, leading to slow response times and outages.
  • Unoptimized resource allocation results in wasted CPU, memory, and storage, leading to inefficiencies.
• Why It Happens:
  • Some servers are not designed for modern workloads and require constant manual tuning to keep up.
  • Older or proprietary Java EE servers often introduce performance limitations that make it harder to scale applications dynamically.
• How a modern GlassFish Server helps:
  • A recent GlassFish server is optimized for high load and maximum throughput
  • GlassFish provides a monitoring service to help investigate and detect performance issues
  • The OmniFish company provides expert services backed by core GlassFish experts to help with troubleshooting and tuning GlassFish in production

---

2. Rising Maintenance & Licensing Costs

• The Problem:
  • Unexpected licensing fees and costly support contracts can make proprietary servers expensive to maintain.
  • Ongoing security patches and updates require manual intervention, adding to operational overhead.
• Why It Happens:
  • Many vendors lock businesses into long-term contracts, making it difficult to migrate or optimize costs.
  • Legacy Java EE servers often lack automation tools, forcing teams to spend time and resources on manual configurations and troubleshooting.
• How a modern GlassFish Server helps:
  • GlassFish provides a command-line tool to automate administration, while an easy-to-use UI interface helps with generating commands for automation
  • Monitoring data about JVM and GlassFish resources are exposed via HTTP or JMX to collect and analyze them in a central place
  • Cloud-deployments are easy with official Docker images and Embedded GlassFish distribution tuned for running microservices
  • GlassFish is an open-source server, free to use without license costs or vendor lock-in
  • Support service by OmniFish is much cheaper than license costs of most proprietary servers, with a huge added value of high-quality support

---

3. Security & Compliance Risks

• The Problem:
  • Frequent vulnerabilities and outdated security protocols put business-critical applications at risk.
  • Ensuring compliance with GDPR, HIPAA, or industry-specific security standards is increasingly difficult.
• Why It Happens:
  • Some Java EE servers do not receive timely security patches, leaving organizations exposed to potential cyber threats.
  • A lack of built-in security features forces IT teams to implement complex workarounds instead of having security as an integral part of the server.
• How a modern GlassFish Server helps:
  • The GlassFish team regularly updates GlassFish components and releases a new version of GlassFish monthly
  • New security protocols are being added to GlassFish, while protocols that become old and insecure or disabled in default configuration
  • Eclipse Foundation acts as a steward of the GlassFish project oversees that GlassFish complies with the modern security policies
  • OmnIFish provides configuration reviews and guidelines on securing GlassFish installations of their customers
  • OmniFish customers receive a configuration template for GlassFish tuned for production, including improved security

---

4. Compatibility & Integration Issues

• The Problem:
  • Many enterprises use multiple Java EE servers alongside various databases, cloud platforms, and DevOps pipelines.
  • Incompatible servers lead to frustrating integration issues, making development and deployment slower.
• Why It Happens:
  • Some servers are too rigid, following proprietary configurations that don’t play well with other tools.
  • Migrating workloads across different environments becomes a challenge when using servers that don’t align with Jakarta EE standards.
• How a modern GlassFish Server helps:
  • GlassFish is compliant with the latest Jakarta EE specifications, which guarantees compatibility with standard solutions and portability of applications, which reduces vendor lock-in
  • GlassFish is tested against and runs on recent Java versions 
  • Deployments to various environments are well supported, with Docker images, Embedded GlassFish, support for external configuration via MicroProfile Config, and many other features
  • OmniFish provides expert help with migrations from legacy servers and older Java versions to the latest GlassFish server

---

5. Limited Developer & Community Support

• The Problem:
  • Lack of skilled developers who are familiar with specific Java EE servers, making it harder to find expertise.
  • Limited community involvement means fewer learning resources and troubleshooting help.
• Why It Happens:
  • Some Java EE servers aren’t actively maintained by an engaged open-source community, leading to slower feature development and fewer online resources.
  • Vendor-controlled solutions restrict developer freedom, limiting innovation and flexibility.
• How a modern GlassFish Server helps:
  • GlassFish is well documented and natively supports recent Jakarta EE and MicroProfile standards, which makes it easier to find resources and reuse knowledge
  • There are actively maintained plugins for GlassFish for all the major Java IDEs
  • As an open-source server, GlassFish allows engineers to study how it works internally, and freely develop solutions that extend its functionality
  • In 2025, there are over 50 contributors to GlassFish project, around 6 active project members, 3 project leads, and many other people that work on external components heavily used by GlassFish, such as EclipseLink, Jersey, or Weld
  • There’s an active community in various discussion channels, and OmniFish engineers are at the core of it, ready to join any discussion, answer questions and provide advice

---

Are You Using the Right Java EE / Jakarta EE Server?

Many IT leaders face these challenges and often the root cause is their current Java EE server. If your organization is experiencing performance struggles, high costs, security risks, or compatibility issues, it may be worth exploring more efficient alternatives, like GlassFish, that better align with modern enterprise needs.

The right Java EE server should be scalable, secure, cost-effective, and seamlessly integrate with your existing infrastructure. Are you confident that yours is meeting those expectations?