Best Sole Proprietorship Accounting Software 2025
Compare accounting software designed for self-employed individuals. Schedule C expense tracking, self-employment tax calculation, mileage deductions, and quarterly estimated tax management.
Understanding Self-Employment Tax (Schedule SE)
Sole proprietors pay 15.3% self-employment tax on net business income. This covers Social Security and Medicare taxes that employers typically withhold from W-2 employees.
2025 Self-Employment Tax Breakdown
| Component | Rate | Income Cap | Notes |
|---|---|---|---|
| Social Security | 12.4% | $176,100 (2025) | Only on net earnings up to cap |
| Medicare | 2.9% | No cap | On all net earnings |
| Additional Medicare | 0.9% | >$200K single | High earners only |
| Total SE Tax | 15.3% | Up to $176,100 | Deduct half on Form 1040 |
Tax-Saving Tip
You can deduct half of your self-employment tax (7.65%) as an above-the-line deduction on Form 1040. This reduces your adjusted gross income even if you don't itemize deductions.
Minimum Threshold
You only owe self-employment tax if your net earnings exceed $400 for the year. Below this threshold, you are not required to file Schedule SE.
Sole Proprietor Software Comparison
Compare features critical for sole proprietorship accounting: Schedule C categorization, self-employment tax calculation, mileage tracking, and invoicing capabilities.
| Software | Price | Best For | Schedule C | SE Tax | Mileage | Invoicing | Reports |
|---|---|---|---|---|---|---|---|
| QuickBooks Self-Employed | $20/month | Mileage & tax tracking | Basic | Limited | |||
| QuickBooks Online | $25/month | Full accounting | Advanced | 80+ reports | |||
| FreshBooks | $21/month | Invoicing & time tracking | — | Excellent | Basic | ||
| Wave | Free | Budget-conscious | — | — | Good | Basic | |
| Zera Books | $79/month | Document processing | — | Export to QBO | Transaction-level |
Schedule C Expense Categories
Your accounting software should categorize expenses to match IRS Schedule C line items. Here are the most common deduction categories for sole proprietors.
Advertising
Facebook ads, Google Ads, business cards, flyers
Car and Truck Expenses
Mileage (67¢/mile 2024), gas, repairs, insurance
Contract Labor
1099 contractors, freelancers, subcontractors
Depreciation
Computer equipment, furniture, vehicles (Form 4562)
Insurance
Liability, professional, health premiums (self-employed)
Legal & Professional
Attorney fees, CPA fees, bookkeeping services
Office Expense
Software subscriptions, supplies, postage
Rent (Vehicles/Equipment)
Equipment leases, vehicle rentals
Rent (Business Property)
Office rent, coworking space, storage
Utilities
Phone, internet, electricity (business portion)
Multiple Businesses?
If you operate more than one sole proprietorship, you must file a separate Schedule C for each business. Good accounting software lets you track multiple businesses under one account.
Bookkeeping Best Practices for Sole Proprietors
Follow these practices to simplify tax filing, maximize deductions, and maintain IRS-ready records throughout the year.
Open Business Bank Account
Separate business and personal finances from day one. Not legally required but essential for clean records.
Save All Receipts
Document every business expense. Use accounting software receipt capture to photograph and store digitally.
Pay Quarterly Estimates
Avoid penalties by paying estimated taxes quarterly: April 15, June 15, September 15, January 15.
Track Mileage Daily
Log business miles immediately. The 67¢/mile deduction (2024) adds up fast for client visits and errands.
Reconcile Monthly
Match bank transactions to accounting records monthly. Catch errors before they compound at tax time.
Calculate Home Office
If you work from home, deduct either actual expenses (Form 8829) or simplified method ($5/sq ft, max 300 sq ft).

“My clients send me all kinds of messy PDFs from different banks. This tool handles them all and saves me probably 10 hours a week.”
Ashish Josan
Manager, CPA at Manning Elliott
QuickBooks Self-Employed vs QuickBooks Online
Many sole proprietors wonder which QuickBooks version to choose. Here's a detailed comparison to help you decide.
QuickBooks Self-Employed
$20/month
- Schedule C tax categorization
- Automatic mileage tracking
- Quarterly tax estimates
- Basic invoicing
Limitations:
- • No double-entry accounting
- • Limited financial reports
- • No 1099 contractor management
- • Cannot scale if business grows
QuickBooks Online Simple Start
$25/month
- Full double-entry accounting
- 80+ customizable reports
- 1099 contractor management
- Mileage + sales tax tracking
- Upgrade path to higher tiers
For just $5/month more, get a complete accounting system instead of a tax-focused tracker.
Frequently Asked Questions
Sole proprietorship accounting software is financial management software designed for self-employed individuals who operate unincorporated businesses. Unlike corporate accounting, sole proprietor accounting flows directly through personal tax returns via Schedule C (Form 1040). Key features include: income and expense tracking aligned with Schedule C categories, self-employment tax calculation (15.3% for Social Security and Medicare), mileage tracking for business vehicle deductions, quarterly estimated tax payment reminders, and receipt capture for expense documentation. Popular options include QuickBooks Self-Employed ($20/month), FreshBooks ($21/month), and Wave (free). The software helps sole proprietors maximize deductions and simplify tax filing since there is no separate business tax return—all business income reports on your personal 1040.
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Simplify Your Sole Proprietorship Bookkeeping
Process bank statements, categorize expenses for Schedule C, and export directly to QuickBooks or Xero. Unlimited conversions for $79/month.
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