Written by
Jonny Stuart
The average company now uses around 106 SaaS applications (BetterCloud, 2026). For smaller firms, the number sits around 42 - which sounds more manageable until you look at what each of those tools is actually doing, and whether it is connected to anything that matters.
In this post
The Four Agency Workflow Pillars
Most agencies we have spoken to do not know what they are spending on tools per month. Not approximately - exactly. Subscriptions accumulate. Free trials convert. One-off purchases become annual renewals. The founder who set up Harvest three years ago left; the tool is still running.
A tool stack audit is not about cutting costs for its own sake. It is about identifying where your stack has gaps (tools you need but do not have), where it has overlap (tools doing the same job), and where it has dead weight (tools nobody uses that still appear on the bank statement).
Done properly, it takes a few hours. Done once a year, it compounds.
The Four Agency Workflow Pillars
Generic SaaS audit guides tell you to inventory your tools, check utilisation, and cut anything below a threshold. That is the right instinct, but the wrong frame for agencies.
The question for an agency is not "is this tool being used?" The question is "is this tool connected to the revenue cycle?"
Agency revenue flows through four pillars: time, projects, billing, and client communication. Every tool in your stack should connect to at least one of them - and ideally to more than one. If it does not, it is overhead.
Use this as your audit frame:
Pillar | What belongs here | What to look for |
|---|---|---|
Time | Time tracking, resource scheduling | Accuracy of logs, billable vs. internal split, manual entry overhead |
Projects | Task management, project planning, scope tracking | Where scope changes get documented, how budget burn is visible |
Billing | Invoicing, quotes, change orders | How long from delivery to invoice, what goes unbilled |
Client comms | Email, Slack, client portals | How many separate environments the team navigates per client |
Anything that does not sit clearly in one of these four pillars deserves a harder look.
Step 1: Build the Inventory
Pull every tool your agency pays for. Include:
Software subscriptions on company cards and expense accounts
Per-seat tools where individuals have their own logins
Annual renewals that appear once a year and get forgotten
Legacy tools kept for one client or one workflow
List each tool, its monthly cost, who uses it, and which pillar it serves. This step typically takes 60-90 minutes and usually produces a number that surprises founders.
BetterCloud's 2025 research found that 53% of SaaS licenses go unused across organisations. For agencies, the most common unused licences are project management tools from a previous era, time tracking tools replaced by a new one without cancelling the old, and collaboration tools adopted for a client's preference and never cancelled.
Step 2: Apply the Keep / Cut / Consolidate Framework
For each tool, ask three questions:
Is it connected to the revenue cycle?
If a tool does not help the agency track time, deliver projects, send invoices, or communicate with clients, it needs a specific justification to stay.
Does it overlap with another tool you already have?
Overlap is common at agencies because tools accumulate organically. Two project management tools. Two time trackers. A CRM that duplicates client data that also lives in the invoicing system. Overlap means paying twice for capability you are only using once.
What would happen if you turned it off tomorrow?
If the honest answer is "probably nothing for a few weeks," that is a signal.
Apply one of three decisions:
Keep: Connected to the revenue cycle, no overlap, actively used. Leave it alone.
Cut: Not connected to revenue, duplicated by another tool, or unused. Cancel.
Consolidate: Doing a job that should be done inside a tool you already have. Migrate and cancel.
Step 3: Audit the Gaps
The audit is not just about what to remove. It is also about what is missing.
The most common gap at agencies running fragmented stacks is real-time budget visibility. Time is tracked in one tool. Project budgets live in another. Billing is in a third. Nobody has a live view of how much budget remains on an active project without running a manual report.
That gap has a cost. It is covered in detail in why agencies lose money on projects - but the short version is that agencies without real-time budget visibility discover project losses at invoice time rather than during delivery, when there is still something to do about it.
If your audit reveals that time data and project budgets are in separate systems with no live connection, that is a gap worth addressing ahead of any cost-cutting.
Step 4: Check the Connections
The most important dimension of an agency tool stack is not the individual tools - it is how they connect.
A time tracking tool that does not feed into project budgets is incomplete. A project management tool that does not connect to invoicing creates manual work at billing time. A CRM that does not share data with the project system means client context has to be rebuilt from scratch by whoever picks up the account.
For each tool you are keeping, ask: does it share data with the other tools it should share data with? If the answer is "we export a CSV" or "someone does it manually," that is a consolidation candidate.
The per-seat pricing article earlier this week touches on this from a cost angle - but it is also worth reading from an operations perspective. Tools that do not connect to each other require a person to connect them, and that person is usually a senior member of the team. See why per-seat pricing punishes growing agencies.
What a Clean Stack Looks Like
A well-audited agency stack typically has fewer tools than expected. The agencies we have spoken to who have gone through this process describe ending up with one or two core platforms rather than seven or eight, and recovering time previously spent navigating between them.
The ideal end state for most 15-30 person agencies is a single platform that covers time tracking, project management, billing, and profitability visibility. Not because consolidation is inherently good, but because each additional tool adds a navigation cost, an integration cost, and a coordination cost that is paid every day by the people doing the work.
AgencyFlo is built as that single platform. Time, projects, billing, and real-time margin visibility - connected from the moment data is entered. Flat pricing at $50/month regardless of team size. Apply for early access: agencyflo.ai
Key Takeaways
The average smaller firm uses around 42 SaaS tools. Most agencies do not know exactly what they are paying per month across all of them.
The right audit frame for agencies is not "is this tool used?" but "is this tool connected to the revenue cycle?" Time, projects, billing, and client comms are the four pillars everything else should connect to.
Around 53% of SaaS licences go unused across organisations. At agencies, the most common dead weight is legacy project management and time tracking tools that were replaced but not cancelled.
The audit should identify gaps as well as cuts. The most common gap is real-time budget visibility - time and project data in separate systems with no live connection.
The goal is a connected stack, not a minimal one. Fewer tools that share data is more valuable than more tools that do not.
Frequently Asked Questions
How do you run an agency tool stack audit?
Start by inventorying every tool the agency pays for, including per-seat subscriptions and annual renewals. Then apply a keep/cut/consolidate decision to each one, using the question "is this connected to our revenue cycle?" as the primary filter. Finally, audit the connections between tools you are keeping to identify where data is being moved manually.
What SaaS tools should an agency cut first?
Any tool that duplicates a capability you already have in another platform, any tool where usage has dropped below 30-40% of the team, and any tool that requires manual data export to connect to the rest of the stack. Legacy project management tools and time trackers are the most common candidates.
How often should an agency audit its tool stack?
Once a year is a reasonable minimum. Quarterly is better if the agency is growing quickly, since new tools tend to accumulate with new hires and new clients.
What are the signs an agency's tool stack has grown too large?
Senior staff spend significant time manually assembling information from multiple tools. New team members take weeks to understand which system is the source of truth. Project budget status cannot be checked in real time without running a report. Billing requires a manual reconciliation step at the end of each month.
What is the difference between a SaaS audit and an agency tool stack audit?
A generic SaaS audit focuses on cost and utilisation. An agency tool stack audit focuses on whether tools are connected to the revenue cycle - time, projects, billing, and client communication. The question is not just "is this being used?" but "does this connect to how we deliver and invoice work?"
