How to Audit SaaS Applications (Without Losing Your Mind)

Martin Snyder
Jul 25
3 min read

SaaS apps have changed how businesses operate. They help teams move faster, collaborate globally, and scale without the burden of heavy infrastructure. But here’s the problem: the same flexibility that makes SaaS so useful also makes it hard to manage—and even harder to secure.

Whether you're a security lead, IT director, or compliance officer, one thing is clear: you need visibility. That’s where SaaS auditing comes in.

In this post, we’ll walk through how to audit your SaaS applications in a way that reduces risk, supports compliance, and actually helps—not hinders—your team.

Step 1: Discover What You’re Actually Using

Most organizations underestimate their SaaS footprint. Shadow IT—apps that employees adopt without IT approval—isn’t just common, it’s the norm. According to a 2023 survey from Productiv, companies use over 200 SaaS apps on average, and nearly half of them are unsanctioned.

How to uncover them:

Check expense reports for subscriptions charged to company cards.
Review browser history and bookmarks (yes, really).
Pull logs from your SSO or Identity Provider.
Use an automated SaaS discovery platform like Waldo Security to identify both managed and unmanaged applications.

Pro Tip: Waldo’s free OAuth Discovery Tool can scan your environment and instantly surface hidden apps that employees have connected to Google Workspace or Microsoft 365 without IT oversight.

Step 2: Analyze the Risk Each App Introduces

Not every SaaS app is created equal. Some store sensitive data or operate with elevated permissions. Others have questionable security policies or unknown compliance postures.

Ask yourself:

Does the app support MFA?
Is the data encrypted at rest and in transit?
Does the vendor comply with frameworks like SOC 2, GDPR, or HIPAA?
Can you manage the app via your SSO?
What happens in the event of a breach?

Waldo Security simplifies this step by automatically flagging apps with elevated scopes, risky permissions, or poor security documentation—so you don’t have to audit each one manually.

Step 3: Audit Access and Permissions

One of the most overlooked SaaS risks? Over-permissioned users.

Employees come and go. Roles change. But rarely does anyone remember to adjust access—or remove it entirely.

During your audit:

Check who has access to each SaaS app.
Review the permissions granted (admin, editor, viewer, etc.).
Identify any former employees or contractors who still have access.
Implement Role-Based Access Controls (RBAC) wherever possible.

Access reviews aren’t fun—but they’re essential. Waldo Security’s permission tracking helps you automate this process and identify anomalies quickly.

Step 4: Eliminate Redundancies and Low-Value Tools

It’s common to find multiple tools serving the same purpose: two project management platforms, three note-taking apps, four file storage solutions.

Ask:

Which apps have low or no usage?
Which tools are duplicative?
Which apps can be consolidated or replaced with enterprise-approved alternatives?

Cutting unnecessary tools saves money, reduces risk, and improves productivity. Less sprawl = fewer surprises.

Step 5: Build Continuous Monitoring into Your Workflow

A SaaS audit shouldn’t be a one-and-done project. New apps are added constantly—especially in fast-moving teams. The best way to stay ahead of SaaS chaos is with continuous discovery and governance.

What this looks like:

Automated alerts for new SaaS connections.
Recurring access reviews.
A lightweight SaaS request/approval process.
End-user education to reduce the growth of shadow IT.

Using Waldo Security, you can implement ongoing monitoring that surfaces changes in your SaaS landscape in real time—before they become problems.

Why Auditing SaaS Apps is a Competitive Advantage

Yes, a solid audit helps you avoid breaches and pass compliance checks. But more importantly, it helps you run a more efficient business. You’ll:

Cut unnecessary spending
Eliminate risky tools
Secure sensitive data
Prove compliance to auditors and investors

SaaS isn’t going away—and neither is the complexity that comes with it. But with the right visibility and tooling, it’s manageable.

If you’re ready to gain control over your SaaS environment, Waldo Security can help. We make it easy to discover, assess, and govern SaaS usage across your entire organization—so security doesn’t get in the way of productivity.