CTMS vs. Spreadsheets: Why Choosing CTMS is Better?

Posted in CTMS

The thought about streamlining clinical trials often pivots around the use of CTMS vs. Spreadsheets. While spreadsheets are a familiar tool and easy to use, it wasn’t built to handle the demands of clinical research. As trials grow in complexity, relying on manual spreadsheets means a lack of automation, limited scalability, and significant regulatory compliance risks.

By making the transition to a centralized Clinical Trial Management System (CTMS), research organizations can free up to 30% of the administrative time that is lost. This allows research centers to allocate their resources effectively, making clinical trials cost-effective, helping accelerate the development of new treatments.

Why is Spreadsheet Still Used To Manage Clinical Trials?

Spreadsheets are often considered the “default” tool in clinical trials, not because they are the best for the job, but because they are the most accessible.

• Perceived Affordability: Most organizations already have a Microsoft 365 license. On the surface, starting a new study in a spreadsheet appears to have a “zero-dollar” entry point compared to the upfront investment of a dedicated Clinical Trial Management System.
• Zero Learning Curve: Almost every professional in the clinical space is already proficient in spreadsheets. There is no need for intensive software training or an “onboarding” period, which allows teams to start logging data immediately.
• Total Autonomy: Research teams can build their own trackers without waiting for IT approval or vendor configuration. This sense of control is highly appealing in the fast-paced startup phase of a trial.

Risks of Relying on Spreadsheets for Clinical Trials

Spreadsheet is easy to use, flexible, and works well when the trial activity is still limited. However, as they scale, sheets like Excel start to create blind spots that are hard to ignore.

1. Data Integrity & Errors

Spreadsheets rely on manual updates and copied formulas with multiple handoffs. Over time, small/insignificant issues, like overwritten cells, version changes, add up. These errors aren’t always obvious, and when they surface late, they can force teams to revisit months of data and decisions.

2. No Compliance Audit Trails

Clinical research requires clear documentation of how data is created, reviewed, and changed. Regulations like 21 CFR Part 11 and ICH E6 (R2) expect full traceability. A spreadsheet doesn’t capture user activity or change history in a reliable, audit-ready way, which puts teams under pressure during inspections and raises questions about data integrity.

3. Fragmented Collaboration

Most trials involve multiple stakeholders, sponsors, CROs, & sites often working across different regions. Sharing a spreadsheet through email or shared folders leads to confusion about which version is current. Teams spend valuable time reconciling files instead of focusing on study execution.

4. Inadequate Oversight

A spreadsheet makes it difficult to get a clear, up-to-date picture of what’s happening across all sites. Tracking enrollment, deviations, adverse events, and protocol issues manually increases the risk of missing trends or delays. Without timely visibility, problems are often addressed only after they escalate.

5. Budget & Payment Chaos

Trial budgets change frequently due to amendments, enrollment shifts, and site-specific agreements. A spreadsheet can track numbers, but it doesn’t handle complex workflows like milestone-based payments or ongoing budget reconciliation well. This often results in delayed payments, manual corrections, and limited confidence in financial reports.

6. No Standardization

When each study team builds its own spreadsheets, consistency is lost. Data fields differ, reporting formats vary, and documentation becomes harder to align across trials. This lack of standardization creates friction as organizations scale and makes cross-study reporting more time-consuming.

Manual CTMS vs. Spreadsheets 

Despite the availability of dedicated software, spreadsheets still remain a competition. Let’s take a look at what each has to offer: 

Feature	Manual Spreadsheets (spreadsheet)	Dedicated CTMS
Data Integrity	High risk of accidental errors like deletions, formula problems, & “copy-paste” mistakes.	Built-in data validation & protected fields to prevent accidental errors.
Audit Trails	Non-existent or easily bypassed. Cannot prove who changed what.	21 CFR Part 11 compliant; every change is logged with a time/user stamp.
Real-Time Oversight	Data is only as current as the last manual update.	Live dashboards show enrollment and site status as it happens.
Collaboration	Version control issues: File names like “Version_FINAL_v2” create confusion.	Single source of truth; all users work in the same live environment simultaneously.
Automation	Entirely manual. You have to remember every deadline yourself.	Automated alerts for expiring docs, upcoming visits, and milestones.
Financials	Manual tracking of site payments; prone to overpayment or missed cycles.	Automated financial modules for milestone-based payments and budget tracking.
Reporting	Hours spent “cleaning” data to create a single report.	One-click reporting for stakeholders, sponsors, and monitors.

What Makes CTMS Software The Right Choice for Trial Management 

A Clinical Trial Management System (CTMS) is designed specifically to support the way trials operate in the real world, bringing structure without sacrificing flexibility.

1. Real-Time Dashboards

CTMS dashboards give teams a live view of enrollment, site activity, timelines, and pending actions. This shared visibility helps teams stay aligned and address risks early, rather than reacting after delays occur.

2. Task Automation

Routine tasks and reminders are built into the system. Alerts for upcoming visits, missing documents, or overdue milestones reduce the need for manual follow-ups and help sites stay compliant with less effort.

3. Site Management

All site-related activities are managed in one place. CRAs can track visits, monitor investigator performance, and document interactions consistently, improving coordination and accountability across sites.

4. Budget & Finance Modules

CTMS provides clearer control over trial finances. Forecasted and actual costs are tracked together, payments can be tied to milestones, and finance teams have a reliable source of truth without relying on fragile spreadsheets.

5. eTMF Integration

Documents are collected and organized as the trial progresses, not at the end. Version control and document tracking support ongoing inspection readiness and reduce last-minute pressure on study teams.

6. Regulatory Compliance

CTMS platforms are built with compliance in mind. User access is controlled, changes are logged, and audit trails are always available. This supports consistent compliance across studies and simplifies audit preparation.

Move Beyond Spreadsheets, See What Folio3 Digital Health Can Do For You

Folio3 Digital Health offers a fully customizable, AI-powered Clinical Trial Management Software built to handle complex workflows of modern clinical trials. It unifies operations, budget, site management, & documentation so your teams stay organized, compliant, and in control at all the stages of a clinical trial.

Whether you’re looking for end-to-end clinical trial software or targeted CTMS workflow automation, explore how Folio3 Digital Health’s Clinical Trial Management Software can support your needs.

Closing Note 

One thing about CTMS vs. spreadsheets is that the latter can support early planning, but they struggle under the weight of larger, more regulated trials. As complexity increases, spreadsheet makes it harder to maintain visibility, consistency, and confidence in the data. A CTMS provides the operational structure needed to manage trials efficiently, stay compliant, and scale without adding unnecessary risk.

Frequently Asked Questions 

How does a CTMS ensure 21 CFR Part 11 compliance compared to a spreadsheet? 

A spreadsheet lacks the architecture for permanent, timestamped audit trails. A CTMS has “closed system” security, requiring unique user IDs, electronic signatures, and a non-editable history of every data change. This ensures that the integrity of your clinical records meets FDA and EMA standards for authenticity and reliability.

Can a CTMS automate the reconciliation between EDC and site payment workflows?

Yes. While spreadsheets require manual cross-referencing of EDC data to trigger payments, a CTMS can integrate directly with EDC platforms. The system automatically verifies when a “Subject Visit” has occurred and triggers the corresponding milestone payment, eliminating the risk of double-payments or manual entry errors.

What is the impact of CTMS on eTMF inspection readiness? 

CTMS vs spreadsheets provide a structured environment where essential documents are linked directly to study milestones. Unlike a spreadsheet, which is a disconnected tracker, a CTMS often features eTMF integration. This means that as site activities are completed, the system automatically flags missing or expiring documents, ensuring you are “audit-ready” at all times rather than scrambling before a regulatory visit.

How do CTMS platforms handle multi-currency site reimbursements for global trials? 

Managing fluctuating exchange rates and country-specific tax requirements in a spreadsheet is a significant risk factor. CTMS vs spreadsheets use localized financial modules that automatically calculate reimbursements based on real-time exchange rates and predefined investigator contracts, providing a level of financial precision that manual sheets cannot match.

How does a CTMS improve data integrity during multisite monitoring? 

Monitoring in a spreadsheet relies on static, disconnected reports. CTMS vs spreadsheets centralizes monitoring logs and follow-up items. When a CRA (Clinical Research Associate) logs a deviation or an issue, it is instantly visible to the study manager. This “single source of truth” prevents the data fragmentation that occurs when multiple versions of a spreadsheet tracker are shared via email.

Is a CTMS worth the investment for a small-scale or Phase I trial? 

Yes. Even for small trials, a CTMS provides a scalable foundation. Starting with a CTMS ensures that as your trial progresses to Phase II and III, your data is already organized, compliant, and ready for larger-scale oversight.

How much time can my team really save by switching from a spreadsheet to a CTMS? 

Industry research, including data from the Tufts CSDD, suggests that teams can reclaim up to 30% of their administrative time. By automating manual tasks like visit tracking, document follow-ups, and payment reconciliation, your staff can focus on patient safety and study quality rather than spreadsheet maintenance.

Why is version control such a big issue with spreadsheets in clinical trials? 

In clinical research, having multiple people editing a spreadsheet file leads to “version chaos.” Without a centralized database, it’s easy to work off an outdated list of subject enrollments or site contacts. A CTMS ensures that every stakeholder, from the sponsor to the CRA, is looking at the same live data simultaneously.

Is a CTMS customizable to fit specific study protocols? 

Yes. The CTMS solution by Folio3 Digital Health is designed to be flexible. While the spreadsheet is “blank,” which feels customizable, it lacks the logic to enforce protocol rules. A CTMS allows you to build study-specific milestones and alerts that guide your team, ensuring that every site follows the protocol exactly as intended.

Is it difficult to migrate existing study data from a spreadsheet into a CTMS? 

Most modern systems allow for bulk data imports. If your data is currently in a structured spreadsheet format, it can typically be mapped and uploaded into the CTMS quite quickly. This allows you to maintain your study’s history while gaining the benefits of automation and compliance moving forward.

How does a CTMS help with patient recruitment and enrollment tracking? 

A CTMS provides real-time enrollment dashboards. You can see exactly which sites are meeting their targets and which are falling behind. This allows study managers to intervene early to keep the trial on schedule.

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