FreshBooks vs QuickBooks: Which One a Freelancer Actually Needs

I spent 6 months on QuickBooks Self-Employed and 3+ years on FreshBooks. I know both tools intimately. And the comparison isn’t as close as review sites make it seem — they’re designed for different priorities.

QuickBooks Self-Employed is a tax estimation tool with basic invoicing. FreshBooks is an invoicing and client management tool with solid bookkeeping.

Which priority matters more to you? That’s your answer. But let me give you the details.

The Head-to-Head

Where FreshBooks Wins (By a Mile)

Invoicing

This isn’t close. FreshBooks invoicing is the best in the freelancer software market. QuickBooks SE invoicing is… it exists.

FreshBooks gives you:

• Beautiful, customizable templates that make clients take you seriously
• Online payments (credit card + ACH) with one-click payment experience
• Automatic payment reminders at custom intervals
• Recurring invoices
• Proposals that convert to invoices with one click
• Client portal where clients see all their invoices
• Deposit/milestone invoicing
• Average payment time on FreshBooks: 11 days for me

QuickBooks SE gives you:

• Basic invoice template with minimal customization
• Online payments (functional but basic)
• Manual reminders (no auto-follow-up)
• No proposals
• No client portal
• Average payment time on QBSe: 16 days for me

The 5-day difference in payment time matters. On $10,000/month in invoices, getting paid 5 days faster means $10K entering your cash flow earlier every month. Over a year, that’s meaningful for a freelancer managing irregular income.

Time Tracking

FreshBooks has a built-in timer. Start it when you begin working, stop when you’re done, it logs to the project. Convert tracked time to invoices. QBSe has no time tracking at all.

When I billed hourly (year 1-2), FreshBooks time tracking was essential. I tried using Toggl alongside QBSe and juggling two apps was annoying enough that it factored into my decision to switch.

Proposals & Estimates

FreshBooks lets you send professional proposals that clients accept online. Once accepted, the proposal converts to a project and eventually an invoice. It’s a complete sales-to-payment pipeline.

QBSe: nothing. You’re creating proposals in Google Docs or a separate tool.

User Experience

FreshBooks feels like it was designed by freelancers. The navigation is organized around how freelancers think: Clients, Projects, Invoices, Expenses. Finding anything takes one or two clicks.

QBSe feels like it was designed by accountants. Navigation is organized around accounting concepts: Transactions, Tax, Reports. Not unintuitive, but not freelancer-native either.

Where QuickBooks SE Wins (Decisively)

Quarterly Tax Estimates

This is QBSe’s reason for existing and it does it brilliantly.

Based on your year-to-date income, categorized expenses, and tax situation (filing status, state, deductions), QBSe calculates your estimated quarterly tax payment. It updates in real time as you categorize transactions.

Open the app → see “Estimated Q2 payment: $3,847” → pay that amount → done.

FreshBooks doesn’t do this at all. I use a Google Sheet to calculate my quarterly estimates based on FreshBooks data. It works, but it requires manual effort every quarter (45 minutes) versus QBSe’s automatic calculation (0 minutes).

For a new freelancer who’s terrified of tax surprises, this feature alone might justify $15/month.

Business/Personal Separation

QBSe’s swipe-to-categorize interface makes separating business and personal transactions almost fun. Every transaction gets swiped: right for business, left for personal. It’s fast, it’s intuitive, and it gives you clean separation even if you’re using one bank account for everything.

FreshBooks does categorization too, but it’s designed for a business account. If you’re commingling personal and business transactions in one account, QBSe handles that mess better.

Mileage Tracking

QBSe has GPS-based mileage tracking. Turn it on, drive, it logs the trip and calculates the deduction. FreshBooks has no mileage tracking — you need a separate app like MileIQ.

If you drive regularly for business (5+ trips/week), this integrated mileage tracking is genuinely useful. At $0.70/mile in 2026, a 20-mile round trip is $14 in deductions. Over a year of regular client visits, that’s hundreds or thousands of dollars.

Price

$15/month vs. $33/month. That’s $216/year difference. For a new freelancer watching every dollar, that gap matters.

TurboTax Integration

If you file with TurboTax, QBSe exports your data directly. Schedule C is pre-populated. Income, expenses, mileage — all transferred. FreshBooks doesn’t have this integration. You export reports and manually enter data (or give it to your accountant).

My Experience: The Timeline

Months 1-8 (Wave): Free, learned the basics.

Months 9-14 (QuickBooks SE): Switched specifically for quarterly tax estimates after my $8K tax disaster. The estimates were accurate and reduced my tax anxiety significantly. But I hated the invoicing. I kept Wave open just for invoices.

Month 15-present (FreshBooks): Switched because running two tools (QBSe for taxes + Wave for invoicing) was ridiculous. FreshBooks handled invoicing AND bookkeeping well enough that I only needed to add a simple spreadsheet for quarterly tax calculations.

The irony: QBSe taught me how to calculate quarterly taxes by showing me the formula for 6 months. Once I understood it, I didn’t need the automated calculation anymore. A Google Sheet does it in 5 minutes.

Decision Framework

Choose FreshBooks if:

• Invoicing is your #1 priority (getting paid faster, looking professional)
• You bill hourly and need time tracking
• You send proposals to clients
• You have 5+ active clients
• You’re comfortable calculating quarterly taxes yourself (or you have an accountant)
• You’re past year 1 and understand the basics of freelance taxes

Choose QuickBooks SE if:

• Tax anxiety is your #1 problem
• You’re in your first year of freelancing and need tax hand-holding
• Your invoicing needs are simple (few clients, basic bills)
• You drive a lot for business (mileage tracking)
• You use TurboTax for tax filing
• Budget is tight and $15/mo vs $33/mo matters

Choose both if:

• You’re insane and like managing two apps (I did this for 6 months. Don’t recommend.)

Choose neither if:

• You’re brand new and broke → Use Wave (free)

The Verdict

For most freelancers past their first year: FreshBooks. The invoicing superiority directly impacts your cash flow, and you can handle quarterly tax estimates with a simple spreadsheet.

For first-year freelancers: QuickBooks SE for the tax guardrails, with a plan to evaluate FreshBooks once you’re comfortable with self-employment taxes.

They’re both good tools solving different problems. The right choice depends on which problem is bigger in your freelance life right now.