If you think that PCI compliance only matters to retailers, your business may not be as secure as you think. Meeting PCI standards is vital for B2C and B2B, from manufacturers and SaaS developers to hospitals and investment firms. How can you overcome common PCI compliance challenges cost-effectively?
The Most Common PCI Compliance Challenges for Enterprises
PCI DSS requirements revolve around 12 key components, or best practices. For some enterprises, PCI DSS challenges are primarily technical, and others struggle with organizational problems.
1. Poor Data Storage Practices
The more organized your sensitive data is, the easier compliance becomes. On the other hand, unaccounted-for payment information is a disaster waiting to happen. If there’s a breach, “missing” cardholder data can make your company liable for PCI fines and penalties, not to mention lawsuits.
Solution: Standardize your organization’s data storage practices and locations. Minimize the sensitive cardholder data you collect and store. SaaS developers should also implement tokenization technology for any recurring payments.
2. Underestimation of PCI Scope
To become PCI compliant, your organization needs to know which requirements are applicable. PCI rules cover the complete cardholder data environment. According to the PCI Security Standards Council, the CDE includes:
- Sensitive cardholder or authentication data
- Workers who come in contact with cardholder data
- Connected technology, including networks, software, and servers
- Business processes, such as retail sales, accounts receivable, and CRM
Some companies have robust cybersecurity around consumer payment apps and e-commerce sales, but they ignore CDE risks in the way they handle B2B customer data. If your organization keeps a client’s payment information on file, the system must comply with PCI DSS.
Solution: Perform a comprehensive data audit and risk assessment when setting up your PCI DSS program. Map all CDE sources.
3. Excessive Audit Channels and Controls
Miscalculation of your PCI scope can also swing in the opposite direction. Of course, there’s nothing wrong with heightened cybersecurity, but if you apply PCI requirements too broadly to your organization, it adds to the cost and complexity of PCI compliance.
Solution: Limit the scope of PCI DSS requirements with network segmentation. Keep the parts of your business that process, store, or handle cardholder data separate from other systems. This allows you to set up stronger cybersecurity layers in a concentrated area.
4. Failure To Map Human Risks to Cardholder Data
Technical safeguards are vital for PCI compliance, but they’re not the only avenue you need to include. Business processes and people also introduce risks. Employee errors and intentional insider threats can compromise PCI DSS protections.
For example, in 2025, a trio of workers from various cybersecurity firms was charged with secretly partnering with a ransomware gang called ALPHV. Under the cover of protecting customers, these bad actors installed malware and extorted millions of dollars.
Solution: Continuous monitoring of your network and system logs is vital for detecting suspicious traffic, both from within and outside the network.
5. PCI DSS Failures From Vendor Noncompliance
PCI compliance also means ensuring that any third-party companies you contract with to handle cardholder data also follow PCI standards. Don’t automatically assume that payment gateways or cloud providers are secure just because they claim to follow cybersecurity best practices.
Solution: Perform ongoing vendor security management, not just sending a questionnaire at the beginning of the relationship. Look for SOC 2 Type 2 or ISO 27001 certification.
6. Outdated Security Controls
Unlike problems related to productivity, PCI compliance challenges are often technical in nature. To understand and navigate this environment, it’s necessary to have the help of cybersecurity professionals who stay up to date with current best practices.
Solution: Perform a comprehensive review of your current security controls. Are you following the latest access control recommendations, like password managers, or do your employees still keep complicated codes on sticky notes?
7. Difficulty Managing Compliance Manually
For many GRC teams, one of the most common PCI DSS challenges is not having enough hours in the day for required tasks. It takes time to review network logs, schedule audits, apply security patches, encrypt files, and verify the security of key backups. And when overwhelmed workers have to choose between fixing an urgent network problem or performing routine PCI tasks, it’s usually PCI compliance that falls behind.
Solution: Use a comprehensive platform such as Compyl to streamline the compliance process. Give compliance personnel access to real-time insights and in-depth visualizations of compliance processes, network resources, and more.
8. High Costs for Audits, Compliance, and Network Security
Depending on the complexity of your network and operations, meeting PCI standards requires quarterly vulnerability scans, continuous network monitoring, encryption technology, and penetration testing. These PCI compliance costs quickly add up. High-volume merchants also need to pay a Qualified Security Assessor to perform an annual PCI compliance validation assessment.
Solution: Instead of hiring an in-house Chief Information Security Officer, some companies rely on virtual CISO consulting services. Compliance automation platforms can reduce the need for external readiness assessments.
9. Forgotten or Uncompleted Tasks
It can come as a surprise how easy it is for company professionals to forget important compliance tasks. Failing to perform necessary vulnerability scans on time is a common PCI mistake. Similarly, tired workers can accidentally overwrite past scan results. Not having a “clean” baseline to compare against can lead to a failed audit.
Solution: Wherever possible, use document or workflow automation to simplify PCI compliance. Automation is good for security because it ensures that records go where they need to and stakeholders receive important reminders on time.
10. Confusing or Incomplete Policies
Clear and practical policies help workers at every level implement better cybersecurity practices. Poorly-explained, confusing, or burdensome policies can tempt workers to ignore the rules, potentially leading to significant PCI DSS violations.
Solution: Involve stakeholders who are connected to cardholder security processes during policy and program creation. Identify time-wasting tasks and PCI compliance challenges, and develop realistic solutions for your organization.
Customizable and Scalable Solutions for PCI Compliance Challenges
Managing PCI DSS compliance doesn’t have to be complicated—or expensive. Compyl unifies your risk, audit, and security data into one automated platform, so your team can stay ahead of compliance issues and focus on protecting what matters most.
Gain complete visibility across your PCI environment, automate repetitive reporting tasks, and reduce the time your team spends chasing audit evidence. Whether you’re mapping PCI DSS controls to HIPAA or ISO 27001, Compyl scales with your business and simplifies every step of compliance management.
Take the next step toward effortless PCI compliance today.
