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Due diligence serves as the buyer’s primary tool for validating financial, operational, and compliance assumptions in a transaction. When documentation is incomplete, inconsistent, or poorly explained, diligence shifts from confirmation to investigation. This change increases scrutiny, extends timelines, and may place transaction value at risk. For sellers, the greatest exposure often stems not from complex issues but from routine records and processes that were never prepared for examination at this level. AAFCPAs advises that clients begin reviewing records and processes early to anticipate questions and reduce potential delays.
In This Article
When Due Diligence Reveals Gaps in Readiness
Buyers enter due diligence expecting confirmation, not discovery. Financial statements should reconcile. Supporting schedules should align with the general ledger. Corporate records should be complete and readily available. When these basics fall short, diligence takes on a different tone. Routine requests begin to generate follow-up questions, and the process slows as buyers work to understand whether gaps reflect oversight or risk.
“One of the most common issues arises in the data room,” says Emily Feeley, CPA, MBA, Director and leader of AAFCPAs’ Business Transaction Advisory practice. “Files are often uploaded without prior review, sometimes by team members unfamiliar with transaction-level scrutiny. Buyers may receive an accounts receivable aging report only to find unexplained credits or balances that do not match the general ledger. Inventory listings may reflect quantities or values management does not regularly reconcile. These inconsistencies do not always signal a problem, but they require explanation. Buyers must resolve every open question before moving forward.”
Staffing constraints often compound these issues. In many transactions, the accounting team is either unaware of the sale process or lacks the capacity to respond to detailed requests on compressed timelines. Reports are generated on demand rather than pulled from established monthly close processes. In some cases, teams are asked to produce subsidiary ledgers or schedules they do not typically review, increasing the likelihood errors go unnoticed. Information may technically respond to a request while failing to reflect how the business actually operates.
Standard due diligence checklists add another layer of complexity. These checklists are typically broad templates designed to apply across industries and transaction types. Without experienced review, sellers may spend time chasing items not applicable to their structure or provide information that does not address the buyer’s underlying concern.
“Missing or inaccessible corporate records often surface late in the process,” adds Richard Weiner, CPA, MST, CM&AA, Tax Partner. “Buyers commonly request formation documents, historical tax returns, and tax election filings, such as an S corporation election and the related IRS approval letter. Difficulty locating them raises questions about documentation discipline and internal controls.”
Taken together, these issues signal a lack of readiness rather than a lack of integrity. Still, the effect is the same. Confidence erodes, timelines extend, and transaction leverage may shift. AAFCPAs advises that sellers adopt a structured approach to data preparation, checklist review, and record organization. Addressing readiness proactively allows buyers to confirm assumptions efficiently and helps preserve negotiating leverage.
Compliance and Operational Issues That Escalate Buyer Concern
“Even when financial records are sound, compliance and operational issues may introduce risk late in the diligence process,” says Emily Feeley. “These issues tend to surface after initial document review, when buyers begin testing assumptions and requesting supporting detail. At this stage, unresolved items carry more weight because they threaten closing timelines and, in some cases, transaction value.”
- Payroll and worker classification is a frequent area of focus. Buyers examine whether individuals are treated as team members or independent contractors and whether payroll taxes were handled consistently. Misclassification, such as issuing Forms 1099 to individuals who function as team members, may create exposure for back taxes, penalties, and amended filings. What appears to be a historical practice quickly becomes a present concern once a buyer assumes responsibility for the business.
- State and local tax compliance raises similar concerns. Buyers often review where the business operates, where revenue is generated, and whether required filings were made in each jurisdiction. Gaps may exist because a company expanded into new states without updating its filing footprint. In these cases, buyers may assess potential exposure or require remediation before closing, including the use of voluntary disclosure programs to address past noncompliance.
- Balance sheet liabilities tied to internal policies also receive close attention. Accrued vacation is a common example. If a company allows team members to accumulate unused time off but has not recorded the related liability, buyers may require an adjustment. The issue is not the policy itself, but the mismatch between stated practices and recorded financials.
- Operational disruption during diligence can further complicate matters. Owners and senior leaders are often pulled into the transaction process at the same time they remain responsible for revenue generation and day-to-day management. When updated financials show flat or declining revenue, buyers may question whether performance is sustainable. This shift can affect both valuation and negotiating posture.
- Contract review introduces additional complexity, particularly when change-of-control provisions or geographic restrictions are involved. Customer, vendor, and team member agreements may include clauses that trigger consent requirements, pricing changes, or termination rights upon a change of control. These provisions are often identified late, when there is limited time to respond. Working with an experienced merger and acquisitions (M&A) attorney will assist with identification and resolution.
- For companies with foreign subsidiaries or international operations, diligence expands further. Buyers may examine local payroll rules, termination requirements, cash repatriation restrictions, and regulatory compliance in each jurisdiction. These considerations vary by country and are often unfamiliar to U.S.-based management teams, increasing the need for advance preparation.
Individually, many of these issues are manageable. When identified late or explained poorly, however, they may slow the transaction and shift leverage at a critical point in the process. AAFCPAs recommends evaluating compliance and operational practices before diligence begins. Proactively addressing payroll, tax filings, contractual obligations, and international considerations before putting the company up for sale helps prevent last-minute complications, supports timely closings, and maintains buyer confidence.
How We Help
AAFCPAs provides comprehensive transaction advisory and M&A brokerage support to guide business owners, investors, and advisors through complex buy- and sell-side transactions. For sellers, we help prepare financials, resolve gaps, and, when needed, perform audits, reviews, or compilations to promote clarity and confidence. Through our brokerage capabilities, we also help match sellers with aligned buyers and strategic partners, prioritizing long-term fit, continuity, and value creation—not just price. Early tax planning—including restructuring, entity shifts, and strategic gifting—positions the business for favorable after-tax results.
Buyers benefit from due diligence support, strategic fit analysis, and deal structure modeling to understand opportunities and risks. By integrating financial oversight, tax planning—including state and local tax—wealth management, and operational cleanup through outsourced accounting and fractional CFO solutions, AAFCPAs delivers a coordinated approach that preserves value, addresses risks, and keeps transactions aligned with broader financial goals.
Frequently Asked Questions About M&A Due Diligence
How far in advance should we start preparing for due diligence?
Begin preparation 6-12 months before going to market. This timeline allows you to identify and resolve documentation gaps, reconcile financial records, address compliance issues, and organize your data room without rushing. Early preparation also gives you time to implement stronger internal controls that buyers expect to see.
What’s the most common mistake sellers make during due diligence?
Uploading documents to the data room without sufficient review or centralized oversight. In many transactions, multiple team members contribute information, often without a designated primary contact responsible for coordination and tracking. As a result, sellers may provide documents that technically respond to requests but do not reflect how the business actually operates or contain unexplained discrepancies. Even when documents are reviewed individually, the absence of clear ownership over what is uploaded, when, and by whom can create confusion, trigger follow-up questions, and raise red flags with buyers.
Can compliance issues really kill a deal?
While compliance issues rarely kill deals outright, they can significantly impact valuation, extend timelines, and shift negotiating leverage to the buyer. Issues like worker misclassification or missing state tax filings may require costly remediation that reduces your net proceeds.
How do we handle due diligence requests when our accounting team is overwhelmed or not fully aware of the potential transaction?
Consider engaging transaction advisory professionals before the process begins. They can help organize records, anticipate buyer questions, and respond to requests efficiently while your internal team focuses on running the business. Additionally, firms like AAFCPAs provide professionals who can augment your existing team.
What happens if we discover problems during due diligence preparation?
Finding issues early is actually advantageous. You can address problems proactively, develop explanations for buyers, or factor remediation costs into your asking price rather than facing surprise adjustments at closing.
Should we hire outside help for due diligence preparation?
Yes, especially if this is your first transaction, if your internal team lacks M&A experience, or if your team is not aware of the potential transaction. Transaction advisors can identify potential issues you might miss and ensure your documentation meets buyer expectations from day one.
These insights were contributed by Richard Weiner, CPA, MST, CM&AA, Tax Partner, and Emily Feeley, CPA, MBA, Director, Transaction Advisory Services.
Questions? Reach out to our authors directly or your AAFCPAs partner.
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