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Bookkeeping

Why Bookkeeping for SaaS Startups Needs a Different Approach

Avigail Feldman
October 24, 2025
5 min read

SaaS companies don’t operate like traditional businesses, and their books shouldn’t either. Unlike one-time sales models, SaaS revenue is recurring, deferred, and often tied to complex billing structures such as annual prepayments, usage-based tiers, or hybrid pricing. That means cash and revenue rarely align neatly.

Contents

    For early-stage founders still managing books in QuickBooks or Google Sheets, this complexity can lead to confusion, misleading metrics, and missed investor trust. Accurate SaaS bookkeeping isn’t just about keeping the IRS happy, it’s about unlocking clear visibility into your business model, margins, and growth trajectory.

    This guide breaks down what makes SaaS bookkeeping unique, the red flags to watch for, and how Function helps startups go from messy books to investor-grade reporting.

    Why SaaS Bookkeeping Is Different

    SaaS models are built on recurring revenue, which means cash comes in regularly, but not always in sync with the service being delivered. You might invoice a client upfront for a 12-month contract, but can only recognize that revenue gradually each month.

    Add to that usage-based pricing or tiered billing, and things get complicated fast. If you don’t structure your books correctly, you could overstate revenue, misclassify liabilities, or lose credibility with investors.

    SaaS bookkeeping demands systems that can track deferred revenue, recognize income accurately, and clearly separate recurring vs. non-recurring revenue streams — the foundation of reliable SaaS metrics.

    Common Challenges in SaaS Bookkeeping

    For founders managing books in-house or with generalist bookkeepers, a few recurring pain points stand out:

    • Deferred revenue tracking: recognizing income too early can inflate performance.
    • Annual contracts, monthly recognition: invoices and earned revenue rarely align.
    • Usage-based or hybrid billing: variable revenue adds complexity to recognition.
    • Churn and credit notes: refunds or cancellations complicate MRR tracking.
    • Expense categorization: R&D, contractor, or software costs must be tagged correctly to calculate margins and burn rate.

    These aren’t just tax compliance issues, they directly affect board reporting, cash flow visibility, and your ability to measure metrics such as MRR, ARR, and net revenue retention.

    Why Accurate SaaS Bookkeeping Matters for Growth

    Clean books = clean decisions.

    When bookkeeping is off, critical SaaS metrics such as gross margin, burn rate, CAC, LTV, and net revenue retention become unreliable, and that undermines both your financial model and your investor story.

    Accurate bookkeeping gives founders the clarity to answer questions like:

    • How much runway do we really have?
    • Which customers are profitable?
    • What’s driving churn or growth?

    If your books are messy, your pitch deck will be too. Solid bookkeeping is the first step to scaling with confidence. 

    When to Upgrade from General Bookkeeping to SaaS-Specific Support

    General bookkeeping works for the first few months — until it doesn’t.

    When you’re:

    • Reporting to investors or a board
    • Scaling multiple pricing or contract types
    • Building financial models or preparing for fundraising it’s time for SaaS-specific bookkeeping that supports your complexity.

    If you’re gearing up for a seed or Series A round, or working with a fractional CFO, upgrading your systems and support becomes essential. Accurate revenue recognition and investor-ready reporting are no longer “nice to have” — they’re deal-critical.

    Key Tools and Processes for SaaS Bookkeeping

    The right tools simplify the chaos. Commonly used systems include:

    • QuickBooks Online for general accounting
    • Stripe or Chargebee for billing automation
    • SaaSOptics or similar tools for revenue recognition

    But tools are only as good as the people using them. Every system should be backed by:

    • A clear chart of accounts tailored to SaaS operations
    • Properly tagged transactions and cost centers
    • Revenue recognition logic that matches contract terms
    • A consistent monthly close and reconciliation process

    For those interested in foundational guidance, the IRS Guide on Accrual Accounting and OpenView’s SaaS Metrics Standards provide helpful context.

    How Function Supports SaaS Bookkeeping

    At Function, we specialize in bookkeeping built for SaaS companies. 

    Our team supports usage-based and tiered pricing models, deferred revenue, and multi-entity reporting. More importantly, we translate your financial data into investor-grade insights that power your next raise.

    We go beyond compliance, we help you:

    • Build clean books that stand up to due diligence
    • Maintain accurate MRR/ARR and cash flow visibility
    • Deliver professional financial reports to your board

    Whether you’re preparing for your next round or scaling your finance stack, we help you see the story behind your numbers.

    👉 Learn more about Function’s Bookkeeping Services or explore how our CFO Services can help you scale faster with confidence.

    Frequently
    asked
    questions

    What is a cash flow forecast for a startup business, and why is it important?

    A cash flow forecast is a projection of your future cash inflows and outflows, helping you predict your cash position over time. It’s critical for decision-making, managing runway, and preventing cash shortages.

    How often should a startup update its cash flow forecast?

    Early-stage startups should review forecasts at least monthly, and more frequently if they’re pre-revenue, fundraising, or growing quickly.

    What’s the difference between profit and cash flow in a startup?

    Profit reflects your income after expenses on paper. Cash flow shows what’s actually in your bank account. You can be profitable but still run out of cash if your revenue is delayed or expenses spike.

    Frequently
    asked
    questions

    Who is required to file Form 1099-NEC?

    Any U.S. business that paid $600 or more to a nonemployee (individual, sole proprietor, partnership, or LLC) for services during the tax year.

    What types of payments require filing Form 1099-NEC?

    Service-based payments like freelance work, consulting, commissions, or attorney fees. Not for product purchases or employee wages.

    What are the penalties for late filing?

    Penalties range from $60 to $310 per form depending on how late you file. Ignoring the form entirely can cost even more—up to $630 per form.

    Frequently
    asked
    questions

    Why is bookkeeping for marketing agencies different from other businesses?

    Because agencies manage a blend of project and retainer income, subcontractors, and tight cash flows, they need more nuanced revenue tracking and expense categorization than product-based businesses.

    What should agencies prioritize when managing their bookkeeping?

    Accurate revenue recognition, clean contractor tracking, expense categorization, and a chart of accounts tailored to how your agency earns and spends money.

    How can agencies keep their bookkeeping organized throughout the year?

    By reviewing reports monthly, staying on top of invoicing and payables, and working with a bookkeeper who understands the specific needs of agencies.

    Frequently
    asked
    questions

    What’s the difference between a debit and a credit in business accounting?

    In accounting, a debit is an entry that increases assets or expenses, while a credit increases liabilities, equity, or revenue. Every transaction affects at least two accounts — one with a debit and one with a credit — to keep your books balanced.

    Do debits always mean money coming in and credits mean money going out?

    Not exactly. It depends on the type of account. For example, debiting an expense means you're spending money, but debiting an asset like cash means you're receiving money. That’s why understanding account types is essential.

    Why do I need to understand debits and credits if I have a bookkeeper?

    Even if someone else handles your books, knowing the basics helps you read financial reports, ask better questions, and make smarter business decisions. It also makes you a stronger communicator with your finance team or investors.

    What’s a T-account, and how does it help?

    A T-account is a simple visual tool used in accounting to show how a transaction affects two accounts. Debits go on the left, credits on the right. It’s a great way to visualize the flow of money and keep things balanced.

    How can I tell if my financial reports are accurate?

    Look for common red flags: negative balances, uncategorized transactions, or mismatched totals. If you’re unsure, it’s worth having a professional review your books to make sure everything aligns before big decisions or tax time.

    Frequently
    asked
    questions

    Why does Josh describe accountants as “storytellers”?

    Josh believes the value of accounting lies in interpretation, not calculation. Tools such as Exce; already do the math—what founders need is someone to explain what the numbers mean and how they impact strategic decisions. That’s why Function focuses on turning data into stories that help drive business forward.

    How is Function designed to scale without losing personal service?

    Josh built Function with intention: hire thoughtfully, delegate wisely, and embed values into every part of the team. Delegation wasn’t easy, but it allowed Function to grow without becoming impersonal. The goal is to deliver high-touch service at scale—and keep founders from burning out trying to do everything themselves.

    What problem is Function solving for startup founders?

    Function addresses a common frustration: most founders are left to interpret their own financial data. Instead of delivering static reports, Function turns numbers into clear, actionable insights that guide decision-making—pushing information to founders rather than making them dig for it.

    How do I get started with Function?

    Getting started with Function is simple. Founders can visit onefunction.com to book an intro call, learn more about the services offered, and see if the team is the right fit. The onboarding process is built to be smooth and tailored—starting with a conversation about your current financial setup, goals, and the support you need to grow confidently.

    What does Function mean by being “the adult in the room”?

    In today’s tougher funding environment, investors expect startups to be more financially disciplined. Function steps in with experienced, unbiased financial guidance to help founders stay focused, meet their targets, and present investor-ready financials.

    Frequently
    asked
    questions

    I’m not making money yet—do I really need bookkeeping?

    Yes. Even if you’re pre-revenue, you’re likely spending money—whether on software, legal fees, marketing, or contractors. Bookkeeping helps you track those costs, stay organized for taxes, and prepare for investor conversations before they happen.

    Can’t I just wait and figure it out later?

    Waiting often creates more problems than it solves. Messy or missing records can lead to costly cleanup, missed tax deductions, or even lost funding opportunities. Getting your books in order early means less stress and smarter decisions from day one.

    What kind of bookkeeping support does a startup actually need?

    It depends on your stage and growth plans. In the beginning, you may just need basic transaction tracking. As you scale, you’ll need deeper insights, reporting, and forecasting. Function grows with you—from clean books to CFO-level strategy.

    How does Function make bookkeeping easier for founders?

    We handle the financial heavy lifting, so you don’t have to. From tracking expenses to CFO strategy insights, Function gives you clean, up-to-date books and actionable information—so you can focus on building, not balancing spreadsheets.

    Frequently
    asked
    questions

    What does a fractional CFO for business startups actually do during fundraising?

    A fractional CFO helps build your financial model, prepare forecasts, clean up your reports, align your pitch with your numbers, and get all the due diligence materials ready. They also help you answer tough investor questions with confidence.

    When should a startup hire a fractional CFO before fundraising?

    Ideally, at least 2–3 months before you plan to start pitching. This gives enough time to get your books in order, build your model, and craft a deck that reflects your financial story.

    How does a fractional CFO improve a startup’s chances with investors?

    Investors fund confidence. A fractional CFO ensures your financials are credible, consistent, and well-prepared, reducing red flags and speeding up diligence. This can significantly improve your chances of getting a “yes.”

    Frequently
    asked
    questions

    Who needs to follow Form 5472 instructions and file the form?

    Any U.S. corporation with at least 25% foreign ownership, and any foreign-owned single-member LLC with U.S. operations, is likely required to file Form 5472, especially if they engage in reportable transactions with foreign entities.

    What kind of transactions require disclosure on Form 5472?

    Common reportable transactions include loans, payments for services, capital contributions, reimbursements, and management fees between a U.S. company and a foreign-related party.

    What happens if I don’t file Form 5472 correctly or on time?

    You could face a minimum of $25,000 penalty per year. If you fail to respond to IRS follow-ups, the penalties may increase. Non-filing can also create issues during fundraising, audits, or acquisitions.

    Frequently
    asked
    questions

    What is QuickBooks, and how does it work for U.S. businesses?

    QuickBooks is accounting software that works through your web browser or mobile app. Small and mid-sized businesses use it to manage their daily finances - from creating invoices and tracking expenses to handling payroll and tax preparation. The software connects with U.S. banks, includes standard tax forms, and integrates with over 650 business applications.

    How much does QuickBooks cost?

    QuickBooks has four main plans:
    Simple Start: $38 monthly
    Essentials: $74 monthly
    Plus: $115 monthly
    Advanced: $275 monthly

    QuickBooks often runs promotions with significant discounts. Additional services like payroll require separate subscriptions. See QuickBooks Online Pricing & Free Trial

    What features does QuickBooks offer?

    The software provides essential accounting and business management tools. Standard features include:

    • Invoicing and payments
    • Expense and bill tracking
    • Inventory management
    • Financial reports
    • Connections with over 650 business apps
    • Multicurrency
    • Payroll (additional subscription)
    • Time tracking (additional subscription)
    How do I move from QuickBooks Desktop to QuickBooks Online?

    Intuit provides a tool to help Desktop users switch to QuickBooks Online. The tool transfers your customers, vendors, account balances, and transactions. Check Intuit's migration guide first, as some advanced features may not transfer over to the online version. See: Migration Tool

    Does QuickBooks work with other business software?

    QuickBooks connects with more than 650 business applications. This includes popular tools for customer management, online stores, project tracking, and tax preparation like TurboTax. These integrations streamline your workflow by connecting your business tools in one system. See: QuickBooks Integrations

    What payment types does QuickBooks support?

    QuickBooks Payments lets you accept credit cards, debit cards, ACH transfers, and Apple Pay. All payments automatically record in your QuickBooks account, eliminating manual entry. Transaction fees apply. See: QuickBooks Payments

    Can I run payroll with QuickBooks?

    Yes, QuickBooks offers payroll as an add-on service with different plans for U.S. businesses. The service handles direct deposits, tax calculations, and IRS filings. All payroll data integrates directly with your QuickBooks accounting. Choose from Core, Premium, or Elite plans based on your needs. See: QuickBooks Payroll Services

    Can it handle international currencies?

    Yes - the Essentials, Plus, and Advanced plans let you work in multiple currencies. QuickBooks handles the exchange rates and tracks any gains or losses from currency changes. See: Multicurrency in QuickBooks

    What reports does QuickBooks generate?

    QuickBooks generates standard financial reports, including:

    • Profit & Loss Statement
    • Balance Sheet
    • Cash Flow Statement
    • Sales by Product/Service
    • Expenses by Vendor
    • Customer Aging Reports

    The Advanced plan includes more customization options for reporting. See: QuickBooks Reporting

    Is my data secure?

    QuickBooks uses bank-grade encryption and automatically backs up your data. Intuit stores everything on secure servers and runs regular security audits. You can also enable two-factor authentication for additional protection. See: QuickBooks Security

    Does it work for freelancers and self-employed individuals?

    QuickBooks offers a separate version called QuickBooks Self-Employed. This version focuses on what freelancers and contractors need most - tracking income and expenses, sending invoices, and preparing for taxes. It connects with TurboTax for easier tax filing. See: QuickBooks for Self-Employed

    Can multiple users access QuickBooks?

    Yes, each plan allows a different number of users:

    • Simple Start: 1 user
    • Essentials: 3 users
    • Plus: 5 users
    • Advanced: 5 users

    You can control what each person can access in the system.

    Can I connect my bank accounts?

    QuickBooks connects directly to your bank accounts and credit cards to import transactions automatically. This keeps your records current and reduces manual data entry. See: Importing Bank Transactions

    Does it support specific industries?

    While QuickBooks works for most general business needs, it doesn't have industry-specific versions. Some businesses, like construction or manufacturing, might need additional apps or integrations for specialized features.

    What if I need help?

    QuickBooks provides support through live chat, phone support, and online tutorials. Advanced plan users get a dedicated account manager. For specialized help, you can work with a certified QuickBooks ProAdvisor. See: QuickBooks Support

    Is there a mobile app?

    Yes, QuickBooks has an app for iOS and Android devices. You can create invoices, track expenses, and log miles from your phone. See: Mobile app

    Does it help with tax preparation?

    QuickBooks helps organize your tax information through expense categorization and tax reports. Its integration with TurboTax makes filing easier for both businesses and self-employed users. See: TurboTax Integration

    Frequently
    asked
    questions

    What do bookkeeping tax services include?

    Tax-focused bookkeeping services include recording all business income and expenses, reconciling bank and credit card accounts, organizing the general ledger, and preparing tax-ready financial reports like the P&L and balance sheet. Some also help with 1099s and coordinate with your CPA.

    How do I know if my books are tax-ready?

    Your books are tax-ready if:

    1. All transactions are categorized correctly
    2. Your accounts are reconciled through year-end
    3. You have no duplicates, missing info, or personal expenses mixed in
    4. Your P&L, balance sheet, and general ledger are clean and complete
    When should I hire a professional for bookkeeping tax services?

    If you're behind on your books, unsure how to prepare reports, or experiencing growth and complexity in your finances, it’s time to hire a professional. Don’t try to clean up months of data right before tax time.

    Start smarter—and make your finances function as one

    Discover how Function streamlines your finances and scales with you at every stage.

    Start with Function