Last reviewed: June 2026
Bonsai’s starter plan runs $17 per month billed monthly, and the professional tier hits $32. If you send proposals, sign contracts, track time, log expenses, and invoice clients all inside one tool, those prices hold up. If your actual workflow is narrower, say you write contracts in Google Docs, bill on net-30 terms, and mainly need to stay current on quarterly taxes, then you are paying for a significant share of features you never open. That is the friction point that sends freelancers searching for purpose-built alternatives: not dissatisfaction with Bonsai exactly, but the realization that their financial needs have become specific enough to outgrow a generalist platform.
This guide breaks Bonsai’s feature set into three specific financial jobs and matches each one to a tool that handles it with more depth: invoicing and accounting via Wave, year-round deduction tracking via Keeper, and quarterly estimated tax calculation via FlyFin. You can browse a broader set of AI finance tools in the AI finance tools directory if none of these three match your exact workflow. The goal here is a decision framework, not a blanket recommendation to switch. Some freelancers are better off staying on Bonsai. Others have already grown past it and just need a cleaner way to think through what comes next.
Key takeaways
- Wave offers free invoicing and double-entry accounting with no monthly subscription, making it a practical starting point for freelancers who want clean books without paying a platform fee.
- Keeper connects to your bank and card accounts throughout the year to surface deductions as they happen, rather than leaving you to reconstruct them during a rushed tax-season sweep.
- FlyFin generates quarterly estimated tax payment recommendations based on your actual income and deductions, and includes access to licensed CPAs for review and filing, a level of tax specificity Bonsai does not match.
- Switching from Bonsai to a combination of focused tools gains you depth per function but adds migration effort, multiple logins, and potentially a higher total monthly cost you should calculate before committing.
What Bonsai Does Well and Where It Falls Short
The strongest part of Bonsai is the workflow it creates from proposal to contract to invoice. You send a proposal, the client approves it, a contract auto-populates with the agreed scope and rate, and that contract ties directly to a project with its own invoice schedule. For a freelancer who onboards new clients every week, that sequence saves real time and reduces the chance of an approved scope being forgotten before the invoice goes out. Bonsai also gives clients a branded portal where they can view proposals, sign documents, and pay invoices without you needing a separate file-sharing or e-signature account.
The tax and accounting side does not match that quality. Bonsai estimates your quarterly tax liability based on the income you log inside the platform, but it does not connect to your full bank and card transaction history or apply detailed Schedule C logic. If you earn $60,000 a year but your deductible expenses live across 3 cards and a business bank account, Bonsai’s estimate will be off by whatever amount those accounts hold. It also does not produce double-entry accounting records, which matters if your accountant needs a profit and loss statement that actually reconciles to your bank activity.
Expense categorization inside Bonsai requires manual effort. You import expenses and tag them, but the software does not proactively scan your transactions and flag potential write-offs the way dedicated tax tools do. For a freelancer with simple, low-volume spending, that is manageable. For someone with mixed personal and business spending across multiple accounts, the gap compounds over time until tax season arrives and you realize how much you missed.
Wave: Free Invoicing With Real Accounting Underneath
Wave offers free invoicing and double-entry accounting with no monthly subscription fee. That is not a limited trial or a stripped-down version of a paid product. You get a full chart of accounts, bank reconciliation, profit and loss reporting, and the ability to create and send unlimited invoices. Payment processing costs extra, around 2.9 percent plus $0.60 per credit card transaction and roughly 1 percent for bank transfers, but the accounting and invoicing software itself costs nothing. See the Consumer Financial Protection Bureau for official guidance.
Double-entry accounting is the feature that separates Wave from Bonsai’s financial layer. When you connect your bank account and categorize transactions in Wave, it builds accounting records that a CPA can actually work with. You can give your accountant direct access to your Wave account and the data will be usable without extensive cleanup. Bonsai does not offer this, which means its financial records work for rough tracking but fall short for producing tax-ready books.
Wave’s invoicing module lets you create invoices with custom line items, set payment terms, turn on automatic payment reminders, and configure recurring invoices for retainer clients. If you have 8 or 10 retainer clients paying monthly, you can automate the billing cycle entirely. The invoice customization is more flexible than Bonsai’s, though neither tool offers the granular layout control of dedicated invoice design software.
What Wave does not do: tax estimation, contract management, time tracking, or mileage logging. You get an accounting and invoicing foundation, not a full freelance operating system. If your main gap with Bonsai is on the financial record-keeping side, Wave fills it directly. If you also need to replace Bonsai’s contract workflow, you will need a separate tool for that piece.
Keeper: Year-Round Deduction Discovery
Keeper costs roughly $16 to $20 per month depending on whether you pay annually, and it focuses on one problem: identifying every business deduction in your transaction history before you lose track of it. The app connects to your bank accounts and credit cards, then uses AI to flag individual transactions as potential write-offs. You review each flagged item and either confirm it as a business expense or dismiss it. Over the course of 12 months, that process builds a categorized deduction log that transfers directly into your tax filing.
The timing advantage here is significant. Most self-employed workers do a deduction sweep in the 2 weeks before their filing deadline, which means they are trying to remember in April whether a software subscription from the previous August was for business or personal use. Keeper’s ongoing review model means you confirm deductions while the context is still fresh. A $49 course you bought in November for a skill you needed for a specific client project is easy to categorize in November. It is considerably harder to remember with confidence 5 months later.
Keeper also offers CPA filing assistance at an additional cost for users who want a professional to review their deductions and submit their return. The AI layer is the core product; the CPA service is an optional upgrade. If you already have a tax preparer you trust, Keeper still earns its subscription because it feeds that preparer cleaner, more complete records than a manual year-end sweep typically produces.
Keeper does not invoice clients, track income, or calculate quarterly payment amounts. It reads your spending to find deductions. You would pair it with Wave for invoicing and income tracking. The 2 tools address different parts of the financial picture without overlapping.
FlyFin: Quarterly Taxes With a Human Backstop
Self-employed workers in the United States are required to make estimated tax payments 4 times a year, on deadlines in April, June, September, and January. Missing or underpaying those estimates results in an IRS penalty that compounds the surprise of an already-unexpected tax bill. FlyFin addresses this directly by analyzing your income and deductions and generating a specific quarterly payment recommendation based on your actual numbers for that period, not a generic percentage applied to gross revenue.
The platform connects to your financial accounts to read income and expenses, applies Schedule C and self-employment tax logic, and produces a payment figure you can act on. That is more precise than the common advice to set aside 25 to 30 percent of gross income, which ignores the deductions that change your effective liability. FlyFin’s calculation accounts for the write-offs you have already categorized, which can move your quarterly number meaningfully.
FlyFin includes access to licensed CPAs as part of its service tier. If you want a human to verify your deductions, review your quarterly estimate, and file your annual return, that option exists inside the platform. The CPA access is what separates FlyFin from a self-serve tax calculator. For freelancers who earn irregular income, whose rates changed mid-year, or who added a new income stream, having a CPA confirm the quarterly number before you pay it reduces underpayment risk in a way that software alone cannot.
FlyFin is narrowly focused on tax. It does not send invoices, manage clients, or do general accounting. You would use it alongside Wave or another invoicing tool, not instead of one. The value is in the quarterly tax calculation and the CPA access, not in building a complete financial operating system.
QuickBooks Self-Employed as a Middle Path
QuickBooks Self-Employed runs around $15 per month and occupies a middle position between a full accounting platform and a generalist freelance tool. It connects to your bank and card accounts, lets you swipe each transaction as personal or business, tracks mileage automatically using your phone’s GPS, and generates a quarterly estimated tax figure based on your categorized income and expenses. If you want a single subscription that covers expense tracking and quarterly tax prompts without contract management or advanced accounting, it is a direct option.
The mileage tracking is one feature that neither Wave nor Bonsai handles as cleanly. If you drive to client sites, co-working spaces, or supply runs, QuickBooks Self-Employed logs those trips and calculates the deductible amount based on the current IRS standard mileage rate. For a freelancer who puts significant miles on a personal vehicle for business purposes, that automatic tracking can surface a deduction that exceeds the $15 monthly subscription cost many times over.
QuickBooks Self-Employed invoicing is functional but limited. You can create and send invoices and accept card payments, but the customization is minimal and the invoice history does not integrate into the full QuickBooks Online ecosystem if you upgrade later. If invoicing volume is high or you need flexible invoice formats, Wave will serve you better on that specific function. QuickBooks Self-Employed is at its strongest when expense tracking and quarterly tax estimates are your primary goals and invoicing is secondary.
The Real Cost of Splitting Your Tools
Running Wave, Keeper, and FlyFin simultaneously means up to 3 subscription fees, 3 sets of credentials, and 3 data sources that do not communicate with each other by default. Keeper at roughly $20 per month and FlyFin at its current subscription rate can together exceed what Bonsai’s professional plan charges. Before you move, add up the actual cost for your specific combination. The total may be higher than you expect, and the financial benefit comes from improved accuracy and better deduction capture, not from paying less per month.
The migration effort deserves a realistic estimate. You will need to export your client list, invoice history, and payment records from Bonsai before closing your account. Wave can import a CSV of clients and invoices, but not every field carries over cleanly. You will need to reconnect your bank and card accounts in each new tool individually. Setting up your chart of accounts in Wave and your deduction categories in Keeper takes time upfront. Plan for at least a few hours of configuration, and do it at the start of a calendar quarter so your records stay aligned from the beginning.
One approach that avoids a full migration: keep Bonsai only for contracts and proposals, where it is strongest, and switch to Wave for invoicing and accounting. Then add Keeper or FlyFin only if your tax situation warrants it. That partial split reduces the contract workflow disruption while giving you better financial records. It does mean paying for both Bonsai and Wave, but you can potentially drop Bonsai to a lower tier if invoicing is removed from your use case inside the platform.
Who Should Switch and Who Should Stay
Stay on Bonsai if proposals and contracts are a daily part of how you operate. The Bonsai workflow from proposal approval to signed contract to linked invoice is efficient, and no combination of accounting and tax tools replicates that client onboarding layer. If you close 5 or more new client engagements per month and need e-signatures tied directly to project records, rebuilding that flow outside of Bonsai is a real downgrade in efficiency, not just a mild inconvenience.
Switch if your financial complexity has grown past what Bonsai tracks. Specifically: if you have income coming from more than 2 sources, if your quarterly tax estimates from Bonsai have been consistently off, or if you have realized at filing time that you missed deductions you never tracked in real time. Those are signals that the generalist approach is costing you money, either through underpayment penalties or through uncaptured write-offs that a purpose-built tool would have caught.
There is also a middle path worth considering. You do not have to make an all-or-nothing choice right now. Keep Bonsai for client management and add one specialized tool to address your single biggest financial gap. If quarterly taxes are the problem, add FlyFin. If deduction tracking is the gap, add Keeper. If accounting depth is the issue, add Wave and shift your billing there. Test one change before you overhaul the entire stack. That incremental approach lets you verify whether the added depth actually improves your outcomes before you commit to a full migration.
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Sources
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Summary
Bonsai still has a place if your workflow leans on proposals and contracts, but for the money side, dedicated tools go deeper: Wave gives you free invoicing and real double-entry accounting, Keeper flags deductions from your bank feed all year instead of at tax time, and FlyFin turns your actual numbers into quarterly payment estimates with a CPA behind them. Before you switch, add up what running Wave, Keeper, and FlyFin together would actually cost against your current subscription, and factor in the time to migrate and manage separate logins.
Frequently asked questions
Is Wave actually free, or does it have hidden fees?
Wave’s invoicing and accounting software carries no monthly subscription fee. The cost comes when you process payments: credit card transactions run around 2.9 percent plus $0.60 each, and bank transfers cost roughly 1 percent. Payroll is a paid add-on with a monthly base fee plus a per-employee charge. If you send invoices and collect payment by check, direct bank transfer outside of Wave, or through a separate payment processor, you can use Wave indefinitely at no charge.
Can Keeper and FlyFin connect to the same bank account at the same time?
Yes. Both tools use read-only connections to your financial accounts and do not interfere with each other. Keeper reads your spending history to flag deductible expenses. FlyFin reads your income and expense data to calculate quarterly tax estimates. Connecting the same account to both is a normal setup. Neither tool initiates transactions or changes anything in your bank account.
How accurate are FlyFin’s quarterly tax estimates?
Accuracy depends on the completeness of the data you connect. If your income and deductible expenses are fully reflected in the accounts you link, the quarterly figure will be closer to your actual liability than a flat-percentage estimate. If you have income that does not flow through connected accounts, such as cash payments or a business account you have not linked, the estimate will be off by that amount. The CPA review tier helps catch those gaps before you submit your payment to the IRS.
What happens to your Bonsai data if you switch?
Bonsai allows you to export invoices and client records in CSV format, and signed contracts can be downloaded as PDFs. Your payment history exports give you the raw numbers for accounting purposes. The contracts remain valid legal documents regardless of the platform, so your records are preserved. What you lose is the ability to create new proposals and contracts inside Bonsai if you cancel or downgrade your subscription, so complete your export before making any account changes.
Do you need both Keeper and FlyFin, or will one cover your tax needs?
They solve different parts of the tax problem. Keeper focuses on finding deductions throughout the year in your transaction history. FlyFin focuses on calculating and scheduling your quarterly estimated payments. If you have only one specific problem, too many missed deductions or consistently underestimated quarterly payments, start with the tool that targets that issue. If both are problems, the 2 together provide coverage that neither offers on its own.
Is QuickBooks Self-Employed better than Wave for freelancers?
They serve different needs. QuickBooks Self-Employed is stronger for mileage tracking, automatic transaction splitting between personal and business, and built-in quarterly tax estimates. Wave is stronger for accounting depth: double-entry records, a full chart of accounts, and reports your accountant can use at filing time. If you need clean books and higher invoicing volume, Wave fits better. If you primarily want a simple expense tracker with quarterly tax prompts, QuickBooks Self-Employed is more direct. Some freelancers use Wave for accounting and add QuickBooks Self-Employed only for mileage tracking during high-driving periods.
