For more than a decade, the life sciences industry has invested heavily in digital clinical operations. CTMS platforms are mature. EDC systems are sophisticated. eTMF has gone mainstream. Yet clinical trial financials—budgeting, accruals, forecasting, site payments, and vendor spend—remain stubbornly broken. What’s more striking is who bears the consequences first: not finance, not procurement, but clinical operations.
Ask any experienced clinical operations leader what slows their trials down, and financial dysfunction will surface quickly—late site payments, disputed invoices, frozen amendments, CRO escalations, and awkward conversations with investigators who are frustrated by delays that ops did not cause and cannot easily fix. Clinical trial financials may sit organizationally under finance, but operationally, they live—and hurt—inside clinical operations.
This is not a tooling problem in the narrow sense. It is a systems-design problem rooted in how the industry still conceptualizes money versus work.
At the heart of broken clinical trial financials is a simple but damaging assumption: that financial management can be layered on after clinical operations are designed and executed. Budgets are built in spreadsheets. Contracts are negotiated in isolation. Accruals are estimated after the fact. Payments are processed once issues surface.
Clinical operations, meanwhile, is executing in real time—activating sites, onboarding vendors, managing enrollment variability, handling protocol amendments, and responding to regulatory delays. These activities generate financial obligations continuously, but the systems that capture the work are not the systems that recognize the financial impact.
The result is a permanent lag between reality and reporting. By the time finance sees a variance, operations has already moved on. By the time an accrual is questioned, the activity that caused it is weeks or months old. This temporal disconnect is the root cause of mistrust between teams—and the reason ops absorbs the frustration first.
Finance experiences broken clinical trial financials as reconciliation problems: unexplained variances, slow closes, audit exposure. Clinical operations experiences them as workflow failures.
Sites stop responding when payments are delayed. CROs escalate when invoices stall. CRAs get dragged into payment disputes they have no authority to resolve. Study timelines slip because contract amendments are frozen pending budget approval. None of this shows up initially as a financial red flag—it shows up as operational friction.
Operations leaders become the de facto intermediaries between finance, sites, vendors, and CROs. They translate financial uncertainty into operational apologies. They chase documentation to justify invoices. They defend accruals they did not calculate. Over time, ops teams start building shadow spreadsheets and offline trackers—not because they want to, but because the official systems do not answer the questions they are being asked.
This is how financial dysfunction silently erodes operational credibility.
One of the most persistent myths in clinical development is that clinical trial financials are primarily a finance problem. In reality, finance can only account for what the system defines. Clinical operations defines the work.
Every meaningful cost driver in a trial originates in operational events: site activation, subject screening, visit completion, protocol deviations, re-consents, amendments, and close-out activities. When financial systems are disconnected from these events, finance is forced to approximate reality using assumptions, averages, and narratives.
Ops teams, meanwhile, know exactly what happened—but have no structured way to express it financially. The organization ends up with two truths: operational reality and financial representation. When they diverge, operations pays the price.
Spreadsheets are often blamed for broken trial financials, but they are symptoms, not causes. Spreadsheets persist because they allow teams to bridge gaps between systems that were never designed to work together.
What breaks at scale is not Excel itself, but governance. Version control collapses. Assumptions drift. Ownership blurs. When a single study becomes a portfolio, and a portfolio becomes global, spreadsheet-based financial management stops being flexible and starts being fragile.
Operations feels this acutely during amendments. A single protocol change can alter site budgets, pass-throughs, visit schedules, and vendor costs across dozens of countries. Without event-driven financial logic tied to operational milestones, every amendment becomes a bespoke reconciliation exercise. Ops teams slow down not because they lack urgency, but because they lack leverage.
Nothing exposes broken financial foundations faster than accruals. In theory, accruals are simple: recognize costs as work is performed. In practice, accruals in clinical trials are often educated guesses driven by CRO forecasts or historical averages.
Clinical operations knows when work actually happens. Finance needs defensible numbers. When accruals are not grounded in real operational events—confirmed visits, completed milestones, verified deliverables—both sides lose confidence. Finance questions the numbers. Ops questions the process.
Over time, accrual conversations become political instead of factual. Ops leaders stop volunteering insight because it rarely changes the outcome. Finance tightens controls, which slows operations further. Everyone loses.
Perhaps the most damaging consequence of broken trial financials is not late payments or messy reconciliations—it is poor decision-making. When operations lacks real-time financial signal, trade-offs become guesswork.
Should a site be kept open longer? Should enrollment be accelerated in one country versus another? Should a CRO change order be approved now or deferred? These are operational decisions with immediate financial impact. Yet most ops leaders make them without visibility into cash flow, burn rate, or forecast sensitivity.
Finance sees the impact later. Ops feels the pressure immediately.
The industry often responds to financial pain by adding controls: more approvals, tighter thresholds, additional reviews. These measures reduce risk on paper but increase friction in practice. They do not address the core issue—that financial systems are not anchored to operational truth.
What works is a different model altogether: treating clinical trial financials as event-driven, not ledger-driven. Budgets, accruals, and payments should be consequences of verified operational milestones, not parallel processes managed after the fact.
This requires financial logic to live where work happens. It requires shared identifiers, shared timelines, and shared accountability between ops and finance. Most importantly, it requires abandoning the idea that financial accuracy can be achieved without operational context.
When clinical trial financials are designed as an extension of clinical operations, something important changes. Ops teams stop firefighting financial issues and start preventing them. Finance stops chasing explanations and starts trusting the data. Sites experience consistency instead of surprises.
This is not about making operations “own” finance. It is about recognizing that operational systems are the only place where financial truth originates. Until the industry embraces that reality, clinical trial financials will remain broken—and operations will continue to feel the pain first.
The future belongs to organizations that unify how they plan work, execute work, and recognize cost. Not because it sounds elegant, but because it is the only model that scales without breaking the people closest to the trial.