Aug 13, 2019 Robert Fenton

What's the Best Quality Management System Software for the Pharmaceutical Industry?

Is your manual, paper-based quality management system driving you crazy?

Not only is the old school method a headache, but it's also likely causing you quality issues because of its ineffectiveness.

While it's technically possible to meet regulatory requirements from the FDA and other agencies using paper-based methods and spreadsheets, it's not easy. Paper-based quality management systems can quickly become cumbersome and slow down productivity compared to electronic systems (eQMS software).

Pharmaceutical startups and scale-ups frequently assume that delaying eQMS adoption is the leanest approach and that it's easy to manage early requirements for documentation and training using paper. We've seen companies make this mistake hundreds of times, and it's one of the reasons Qualio will help your organization move from a paper-based QMS to our cloud eQMS platform for free.

But, let's not get ahead of ourselves. We might not be the best fit for your company.

Let's take a look at the best QMS software options for your pharma company. Finding a right-sized system is critically important, so we'll provide you with reviews from real users and insight into who is best served by each of these leading options.

The 4 Best Quality Management System Software Options for Pharmaceutical Companies

The best quality management system software option for your pharmaceutical company isn't the best for everyone else.

There is no such thing as a globally best pharmaceutical QMS software, and anyone who tells you otherwise is mistaken. The "best" solution for a startup is not the "best" solution for a giant pharma enterprise with a market portfolio that contains hundreds of approved drugs. The "best" is highly subjective and should be tailored to a company's firmographic profile.

What defines the best for you, then?

Aside from compliance and functionality, the right solution should be tailored to your company’s size--including users, talent resources to administer the software and your budget. It should fit your needs and goals, whether your goals are rapid growth and scaling or global control.

Not every pharma QMS software fits every use case, which is why your search for the right solution should include an evaluation of your own needs.


Qualio is a cloud-based quality management system designed specifically for the needs of startups and small to mid-sized businesses (SMB) in highly regulated life sciences industries, such as pharma.

Qualio offers an intuitive user experience and simple implementations with a design that's built to scale with fast company growth. Qualio is centered around quality document management with features for global collaboration and built-in features to create documents such as policies, SOPs, and other required documentation.

It offers the right balance of flexibility and control with workflow tools, document versioning, training tools, and customized notifications. It also provides support for CAPA, customer complaints, audits, and other vital aspects of the pharma quality management lifecycle.

For information regarding Qualio pricing, please schedule a free product demonstration.

Users on Capterra report high satisfaction with Qualio's ease-of-use, compliance features, and customer support.

Rob from eHealth technologies writes, "it's all right there, easy to learn and easy to teach!" Jonas from Cardiaccs reports his organization was able to begin driving quality quickly after adopting Qualio, stating "without Qualio we would not have been able to achieve our critical milestone of ISO 13485 certification before the end of 2015."

Users report satisfaction with the system, with one user reporting a greater desire for sophisticated business intelligence capabilities within the software. However, the same user notes "I do know [Qualio is] working on this, however, and generally at the startup level, you're not yet in need of super detailed reporting within your QMS yet anyway."

Qualio may be the best fit for your organization if you're a pharmaceutical startup, scale-up, or SMB who is trying to transition away from a paper-based QMS to cloud software efficiently.

Qualio is built for strong document management capabilities and global collaboration and offers complimentary support to first-time adopters of QMS systems. If your paper-based solutions are inhibiting your aggressive growth goals or visibility into compliance, Qualio can provide a fast track to cloud-based value.

Schedule a demo of Qualio today.



SmartSolve is a Pilgrim QMS product produced by Iqvia, a global software firm. This solution is designed to “automate and simplify” common quality management challenges in the pharmaceutical vertical. This includes a product focus on managing risks which occur across the quality environment, document control processes, regulatory climate, and supplier network.

The product is built with workflows for managing documents and processes and includes support for compliant eSignatures, audit trails, and dashboards.

Pricing for Pilgrim is not provided online by the vendor, and limited third-party pricing data is available online. One third-party source reports Pilgrim pricing starts at $542 per one-time user license. The client portfolio includes many prominent global life sciences enterprises, including Abbot, the American Red Cross, the Centers for Disease Control (CDC), and Medela.

User reviews on Capterra praise Pilgrim for its status as an "industry leader for quality applications," including advanced enterprise planning capabilities. Other reviewers note the vendor provides "clear, organized" documentation for system admins.

Other users report a need to attend in-person training classes such as an Administrator Bootcamp offered by the vendor to understand the complex system fully. Also, users say that their organization's version isn't "streamlined" since they haven't adopted all the available modules.

Pilgrim may best serve your company if you're a major global enterprise with the resources to dedicate one or more full-time system administrators to become experts in the QMS software. Users are most satisfied with the "full off-the-shelf version," which is another indicator that Pilgrim is the best fit for global enterprises who need full QMS functionality for post-market approval processes. 

New call-to-action



MasterControl solutions are a well-known name in enterprise quality management software for the life sciences industry. Adopting organizations include five of the largest regulatory agencies in the US.

MasterControl’s mission is to create software-as-a-service (SaaS) products which help pharma and life sciences organizations bring products to market faster with solutions for the entire pharma lifecycle. Cloud-based tools include document management, training, CAPA, validation, and more.

Limited pricing data on MasterControl is available online, although one third-party source says the pricing per user license starts at $1,000 per month. The vendor also offers specialized pricing packages for small businesses which are significantly cheaper, but these small business subscriptions can offer significantly limited functionality. For example, the "Basic" small business package priced at $109 per user per month provides access only to document management and PDF capabilities with no support for training, audits, or risk management.

One full-time system administrator for MasterControl at a large government agency reports high satisfaction with the system and notes the agency always receives "high marks for system" during audits. Other users report high satisfaction with the speed and availability of MasterControl's customer support.

Users also note a particularly "steep" learning curve, noting "this is not a drag-and-drop, push-to-install software. You need a trained System Administrator." Other users report struggles with the high degree of system flexibility, and a need to fully retrain staff on how to use the software every two years.

MasterControl may be the "best" option for your organization if your quality management processes and requirements are intensive enough to justify appointing a full-time system administrator, and you have the resources to commit to an intensive implementation and staff training.

MasterControl is widely-adopted by agencies and enterprises who need comprehensive enterprise software. While the brand offers small business solutions, these lower-priced options still must be configured and come at the cost of functionality.

FREE GUIDE: The Perfect Quality Assurance Plan for Pharmaceutical Companies


QT9 is a quality management software for the enterprise which is compliant with ISO 9001, ISO 13485, and FDA current Good Manufacturing Practice (cGMP). The brand offers both cloud and premises-based deployments, and advertises a "user-friendly application."

QT9 features are designed to fit full enterprise QMS requirements in the pharmaceutical industry by offering support for document control, CAPA, training, audits, supplier quality, and more. The vendor does not provide data on product pricing, and no reports of pricing are available on third-party review websites. However, QT9 is generally priced and sold according to a SaaS subscription model.

While QT9 offers built-in support for the regulatory requirements of organizations in the pharmaceutical industry, it's not a QMS which is specially designed for the life sciences. The vendor serves organizations in less highly regulated industries as well as customers in pharma. User reviews on Capterra reflect QT9's adoption at manufacturing, packaging, and food organizations, with one user reporting "QT9 is more expensive than the cheaper brands."

Adopters report satisfaction with the tool. One user from a small valve manufacturing organization stated: "it's definitely a step up from using spreadsheets!" Other users report a positive experience with QT9 sales and customer support teams.

Users report dissatisfaction with the product being "stiff" and painful to customize, including a lack of functionality for custom reporting. Other users discuss complicated, time-consuming document management workflows, including slow document uploading and a lack of functionality for custom notifications. The system does not support text-based searches for documents.

QT9 may be the right fit for your organization if you have a limited desire for flexibility in your QMS software and minimal document management needs. While QT9 is built for life sciences compliance, it may not be sufficiently flexible to handle the demands of organizations who are subject to various regulatory requirements. It may also not provide sufficient search functionality or streamlining for organizations who manage a high volume of documents.


How to Transition from a Paper-Based QMS to Cloud Software

If you are considering making the transition from a paper-based QMS to a cloud solution, you've probably already experienced dissatisfaction with your current way of doing things.

Chances are you want to adopt a cloud solution which can be implemented quickly and painlessly and begin driving quality and value with the new system as soon as possible. You're most likely to achieve this result by prioritizing pharma QMS vendors who specialize in solutions for small-to-mid-sized businesses and companies with a proven track record of helping companies get off paper.

Evaluate vendors to determine which pharma QMS is the best fit for your size, stage, and budget. Ask prospective vendors for customer success stories at organizations that resemble your own. Prioritize potential software providers who offer high-quality onboarding services and seamless implementations to begin driving value with cloud QMS as soon as possible.

Schedule a demo of Qualio today.

The #1 eQMS for medical device, pharma, and biotech companies

Learn from the best in quality.  Download your guide now.

Published by Robert Fenton August 13, 2019