QuickBooks for Small Business: Complete Setup & Usage Guide
What You'll Learn:
- • How to set up QuickBooks Desktop for your small business from scratch
- • Create and manage your chart of accounts, customers, and vendors
- • Invoice customers, track expenses, and manage cash flow
- • Reconcile bank accounts and generate financial reports
- • Best practices and common mistakes to avoid
Why QuickBooks for Small Business?
QuickBooks Desktop is the #1 accounting software for small businesses in the United States, used by over 4.5 million companies. Whether you're a sole proprietor, LLC, partnership, or corporation with 1-25 employees, QuickBooks provides professional accounting capabilities without the complexity of enterprise software.
Key Benefits for Small Businesses
- Complete Financial Management: Track income, expenses, inventory, payroll, and taxes all in one place
- Professional Invoicing: Create branded invoices, track payments, and send automatic payment reminders
- Tax Preparation Ready: Automatically categorize transactions and generate reports your accountant needs
- Real-Time Cash Flow Visibility: Know exactly how much money you have, owe, and are owed at any moment
- Multi-User Access: Allow your bookkeeper, accountant, or business partner to access the file simultaneously
Choosing the Right QuickBooks Version
QuickBooks offers several versions. For most small businesses, here's what you need to know:
QuickBooks Desktop Pro
RECOMMENDEDBest for: Sole proprietors, freelancers, and businesses with 1-3 users
- • Unlimited customers, vendors, and transactions
- • Invoicing, expense tracking, and basic reporting
- • Bank reconciliation and receipt capture
- • Up to 3 simultaneous users
- • Cost: ~$549/year (one-time license available)
QuickBooks Desktop Premier
Best for: Growing businesses needing industry-specific features (retail, manufacturing, contractors)
- • Everything in Pro, plus:
- • Industry-specific reporting and features
- • Advanced inventory tracking
- • Job costing for contractors
- • Up to 5 simultaneous users
- • Cost: ~$799/year
QuickBooks Desktop Enterprise
Best for: Businesses with 10+ employees, complex inventory, or multiple locations
- • Everything in Premier, plus:
- • Support for 30+ simultaneous users
- • Advanced inventory and pricing rules
- • Enhanced reporting and customization
- • Cost: Starting at ~$1,868/year
Our Recommendation
For small businesses just starting out with 1-10 employees, QuickBooks Desktop Pro Plus is the sweet spot. It provides all essential features at a reasonable price, and you can upgrade later if needed.
Initial Setup & Company File Creation
- Download QuickBooks from the official Intuit website or use your installation CD
- Run the installer as Administrator (right-click → "Run as administrator")
- Follow installation wizard prompts
- Enter your license and product number when prompted
- Restart your computer after installation
Windows Requirements: QuickBooks Desktop requires Windows 10 or Windows 11. Mac users should use QuickBooks for Mac (separate product) or QuickBooks Online.
When you first launch QuickBooks, you'll be prompted to create a company file:
- Click "Create a new company" or File → New Company
- Choose the Express Start option (easier for beginners)
- Enter your business information:
- - Company name (appears on invoices)
- - Industry (QuickBooks suggests accounts based on this)
- - Business type (Sole Proprietor, LLC, Corporation, etc.)
- - Tax ID / EIN
- - Contact information
- Select your fiscal year start date (typically January 1 or July 1)
- Choose a secure location to save your company file (.QBW)
- - Recommended: C:\Users\Public\Documents\QuickBooks\
- - For multi-user: Shared network folder on server
Important: File Location
Your company file location is critical:
- • Single-user: Store locally on your computer
- • Multi-user: Must be on a dedicated server or host computer
- • Never: Store on Dropbox, OneDrive, or cloud sync folders (causes corruption)
- • Backup: Always keep backups in a separate location
Before entering data, configure essential preferences (Edit → Preferences):
Accounting Preferences:
- • ✅ Enable "Use account numbers" (easier for accountants)
- • ✅ Set "First month of fiscal year"
- • ✅ Choose cash or accrual accounting basis
- • ✅ Enable class tracking if you have multiple departments/locations
Sales & Customers Preferences:
- • Choose invoice template (customize later)
- • Set default payment terms (Net 30, Net 15, Due on receipt)
- • Enable automatic payment reminders
- • Configure sales tax if applicable to your business
Bills & Expenses Preferences:
- • Set default bill payment terms
- • Enable tracking of billable expenses
- • Configure vendor 1099 tracking (for tax reporting)
Setting Up Your Chart of Accounts
The Chart of Accounts is the backbone of your accounting system. It's a list of all accounts where you track money coming in and going out. QuickBooks creates a default chart based on your industry, but you'll want to customize it.
What is the Chart of Accounts?
Think of it as filing cabinets for your money. Each account is a drawer where you categorize different types of income, expenses, assets, and liabilities. Example: "Office Supplies Expense" or "Checking Account".
- Go to Lists → Chart of Accounts
- Or press Ctrl + A (keyboard shortcut)
- Review the default accounts QuickBooks created
Your checking, savings, and credit card accounts. These appear on your Balance Sheet.
Examples: Business Checking, PayPal Account, Business Credit Card
Revenue from sales and services. These appear on your Profit & Loss statement.
Examples: Product Sales, Service Revenue, Consulting Income
Business costs and operating expenses. These also appear on Profit & Loss.
Examples: Rent, Utilities, Office Supplies, Advertising, Payroll
- • Accounts Receivable: Money customers owe you
- • Accounts Payable: Money you owe vendors
- • Fixed Assets: Equipment, vehicles, property you own
- • Equity: Your ownership stake in the business
To add accounts specific to your business:
- In Chart of Accounts, click the "Account" button at bottom-left → "New"
- Select account type (Income, Expense, Bank, etc.)
- Enter account details:
- - Account Name: Be specific (e.g., "Google Ads Marketing" not just "Marketing")
- - Account Number: Optional but recommended (e.g., 5100 for Income, 6200 for Expenses)
- - Description: Internal note about what goes in this account
- - Subaccount: Check this if it's a subcategory of another account
- Click "Save & Close"
Recommended Accounts for Small Businesses:
Income:
- • Product Sales
- • Service Revenue
- • Consulting Fees
- • Interest Income
Expenses:
- • Rent or Lease
- • Utilities
- • Office Supplies
- • Marketing & Advertising
- • Insurance
- • Professional Fees
- • Software Subscriptions
- • Travel & Meals
Important: Don't Overdo It
Start with 15-30 accounts. You can always add more later. Too many accounts makes bookkeeping complicated. Too few and you lose visibility into spending patterns.
Adding Customers & Vendors
Adding Customers
Customers are individuals or businesses that buy from you. You need to set them up before invoicing.
- Go to Customers → Customer Center
- Click "New Customer & Job" → "New Customer"
- Fill in customer information:
- - Customer Name: How they appear in your system
- - Company Name: Business name (if applicable)
- - Contact Info: Email (for invoicing), phone, address
- - Payment Terms: Net 30, Due on receipt, etc.
- - Credit Limit: Optional maximum they can owe
- - Tax Settings: Are they taxable? Which rate?
- Add notes about the customer in "Additional Info" tab
- Click "OK" to save
Pro Tip: Use consistent naming. Example: "Smith, John" or "Acme Corp - John Smith". This makes it easier to find customers as your list grows.
Adding Vendors
Vendors are individuals or businesses you buy from (suppliers, contractors, service providers).
- Go to Vendors → Vendor Center
- Click "New Vendor"
- Fill in vendor information:
- - Vendor Name: How they appear in your system
- - Company Name: Official business name
- - Contact Info: Email, phone, address
- - Payment Terms: When they expect payment
- - Tax ID: Needed for 1099 reporting (if applicable)
- - Account Number: Your account number with them
- On "Tax Settings" tab, check "Vendor eligible for 1099" if they're a contractor
- Click "OK" to save
1099 Reporting Reminder
If you pay a vendor $600+ per year for services (not products), you must send them a 1099-NEC tax form. QuickBooks can generate these automatically if you enable 1099 tracking.
Setting Up Products & Services
Products and Services (called "Items" in QuickBooks) are what you sell. Setting these up correctly makes invoicing much faster.
- Go to Lists → Item List
- Click "Item" (bottom-left) → "New"
- Select item type:
- - Service: For services you provide (consulting, hourly work)
- - Non-Inventory Part: For products you don't track quantity (office supplies)
- - Inventory Part: For products you stock and track (requires inventory feature enabled)
- - Other Charge: For fees like shipping, handling, late fees
- Fill in item details:
- - Item Name: What appears on invoices
- - Description: Longer explanation for customers
- - Rate/Price: How much you charge
- - Account: Which income account this goes to
- - Tax: Is this item taxable?
- Click "OK" to save
Example Items:
Service Item: "Consulting Hour"
Description: Professional consulting services
Rate: $150/hour
Account: Service Revenue
Product Item: "Widget Model A"
Description: Premium widget with advanced features
Price: $499
Account: Product Sales
Time-Saving Tip
Create items even for one-time services. It makes invoicing faster and helps you track what you're selling most. You can always edit prices on individual invoices.
Invoicing & Receiving Payments
Once you have customers and items set up, you're ready to invoice and get paid.
- Go to Customers → Create Invoices
- Select customer from dropdown (or add new)
- Choose invoice template (customize later in Templates → Customize)
- Set invoice date and due date (auto-fills based on payment terms)
- Add items/services:
- - Click in the "Item" column and select from your items list
- - Enter quantity
- - Rate auto-fills but can be changed
- - Add description if needed
- Review subtotal, tax (if applicable), and total
- Add customer message (e.g., "Thank you for your business!")
- Click "Save & Close" to save without sending, or:
- Click "Save & Send" to email invoice immediately
Customizing Invoice Templates:
- 1. Go to Lists → Templates
- 2. Right-click your invoice template → Duplicate
- 3. Right-click the copy → Edit Template
- 4. Click "Manage Templates" to add your logo
- 5. Customize colors, fonts, and layout
- 6. Add/remove fields (PO number, shipping info, etc.)
When a customer pays, you need to record it:
- Go to Customers → Receive Payments
- Select customer from dropdown
- QuickBooks shows all unpaid invoices for that customer
- Enter payment amount and date
- Select payment method (Check, Credit Card, Cash, ACH, etc.)
- Check the invoice(s) being paid
- If paying partial amount, QuickBooks asks if you want to:
- - Leave as underpayment: Invoice stays open for balance
- - Write off difference: Close invoice and record discount
- Click "Save & Close"
Pro Tip: For credit card payments, note the last 4 digits in the check/reference number field. This helps match transactions during bank reconciliation.
Stay on top of who owes you money:
- Run "Accounts Receivable Aging Summary" report (Reports → Customers & Receivables)
- Shows invoices by age: Current, 1-30 days, 31-60 days, 61-90 days, 90+ days
- Send payment reminders:
- - Customers → Create Statements
- - Or use built-in email reminders (Edit → Preferences → Send Forms)
- For seriously overdue invoices, consider:
- - Personal phone call
- - Payment plan arrangement
- - Collections agency (last resort)
Tracking Expenses & Bills
Properly tracking every business expense is critical for tax deductions and understanding profitability.
For expenses you've already paid (credit card, check, cash):
- Go to Banking → Write Checks (even if it wasn't a check)
- Or Banking → Enter Credit Card Charges
- Select the bank account or credit card you paid from
- Select vendor (or add new)
- Enter date and amount
- In the "Expenses" tab, select the expense account (e.g., "Office Supplies")
- Add memo describing the purchase
- Attach receipt image (if using receipt capture feature)
- Click "Save & Close"
Receipt Management
QuickBooks Desktop can capture receipts with a mobile app or email. This makes expense tracking much easier and provides documentation for IRS audits.
For bills you've received but haven't paid yet:
- Go to Vendors → Enter Bills
- Select vendor
- Enter bill date and due date
- Enter amount
- Select expense account
- Add memo/reference number
- Click "Save & Close"
This records the expense now but doesn't affect your bank balance until you pay it.
When to Use Bills vs. Expenses:
- • Use "Enter Bills": For vendor invoices you'll pay later (utilities, rent, vendor invoices)
- • Use "Write Checks": For immediate payments (cash purchases, paid invoices)
When you're ready to pay bills you've entered:
- Go to Vendors → Pay Bills
- QuickBooks shows all unpaid bills
- Check the bills you want to pay
- Select payment date
- Select payment method (Check, Credit Card, ACH)
- Select which bank account to pay from
- Click "Pay Selected Bills"
QuickBooks automatically marks bills as paid and records the bank transaction.
Tax Deduction Tips
- • Be detailed: "Marketing expense" is vague. "Google Ads - January Campaign" is specific.
- • Separate personal from business: Never mix personal and business expenses in the same account
- • Track mileage: Use QuickBooks mobile app or separate mileage log
- • Home office: If you qualify, track home expenses separately
- • Meals & Entertainment: Note the business purpose and who you met with
Bank Reconciliation
Reconciling your bank account ensures your QuickBooks records match your actual bank balance. Do this monthly at minimum.
Why Reconciliation Matters
Reconciliation catches errors like duplicate entries, missing transactions, or bank fees you forgot to record. It's your quality control check. Most accounting errors are caught during reconciliation.
- Go to Banking → Reconcile
- Select the bank account to reconcile
- Enter statement ending date (from your bank statement)
- Enter statement ending balance (from your bank statement)
- Click "Continue"
- QuickBooks shows two lists:
- - Left side: Deposits and credits
- - Right side: Checks and payments
- Check off each transaction that appears on your bank statement
- Watch the "Difference" amount at the bottom:
- - $0.00: Perfect! You're reconciled
- - Not $0.00: Something doesn't match
- If difference is NOT $0.00, common causes:
- - Missing transaction (forgot to record something)
- - Wrong amount entered
- - Duplicate entry
- - Bank fee not recorded
- - Transaction dated wrong month
- Once difference is $0.00, click "Reconcile Now"
- Save or print the reconciliation report (keep for records)
Pro Tip: Use bank feeds (download transactions from your bank) to make reconciliation faster. Set it up under Banking → Bank Feeds → Set Up Bank Feed.
Reconciliation Troubleshooting:
- • Off by exact transaction amount? You probably forgot to check it off
- • Off by double an amount? Likely a duplicate entry
- • Off by odd amount? Check for typos in transaction amounts
- • Can't find the problem? Click "Leave" and try again later with fresh eyes
Payroll Setup (Optional)
If you have employees (not just yourself), you'll need to set up payroll. QuickBooks offers payroll as an add-on service.
Payroll is Complex - Consider Getting Help
Payroll involves tax withholding, tax deposits, quarterly filings, W-2s, and penalties for mistakes. Most small businesses either use QuickBooks Payroll service ($45-125/month) or outsource to a payroll company like ADP or Gusto.
Option 1: QuickBooks Payroll (Recommended)
- • Integrates directly with QuickBooks Desktop
- • Handles all tax calculations, deposits, and filings
- • Provides W-2s and 1099s at year-end
- • Employee self-service portal
- • Direct deposit capability
- • Cost: $45-125/month + $5/employee
To enable: Go to Employees → Payroll Center → Sign Up
Option 2: Manual Payroll
You can track payroll manually in QuickBooks, but YOU are responsible for:
- • Calculating federal, state, and local taxes
- • Making tax deposits on time
- • Filing quarterly 941 forms
- • Filing annual 940 (FUTA) forms
- • Providing W-2s to employees by January 31
Not Recommended
Manual payroll is error-prone and time-consuming. Payroll tax penalties are severe (25-100% of underpayment). Unless you're a payroll expert, use a service.
Option 3: Third-Party Payroll Service
Use ADP, Gusto, Paychex, or similar service, then record payroll totals in QuickBooks:
- • Payroll service handles all compliance and payments
- • You get a summary report each pay period
- • Enter totals as a journal entry in QuickBooks
- • Good option if you already use a payroll service
Financial Reports & Analysis
Reports are where QuickBooks becomes powerful. They show you the financial health of your business at a glance.
Essential Reports Every Small Business Should Run
1. Profit & Loss (Income Statement)
Shows: Revenue minus expenses = profit (or loss)
When to run: Monthly and annually
Location: Reports → Company & Financial → Profit & Loss Standard
What to look for: Are you profitable? Which expense categories are highest? Is revenue growing?
2. Balance Sheet
Shows: What you own (assets) vs. what you owe (liabilities)
When to run: Monthly and annually
Location: Reports → Company & Financial → Balance Sheet Standard
What to look for: Are assets increasing? Is debt manageable? Equity growing?
3. Accounts Receivable Aging Summary
Shows: Who owes you money and how overdue they are
When to run: Weekly
Location: Reports → Customers & Receivables → A/R Aging Summary
What to look for: Invoices over 60 days need follow-up. High receivables = cash flow problems.
4. Cash Flow Statement
Shows: Cash coming in and going out over time
When to run: Monthly
Location: Reports → Company & Financial → Statement of Cash Flows
What to look for: Cash flow problems before they become critical. Seasonal patterns.
5. Expense by Vendor Summary
Shows: How much you're spending with each vendor
When to run: Quarterly
Location: Reports → Vendors & Payables → Expenses by Vendor Summary
What to look for: Identify biggest expenses. Opportunities to negotiate better rates.
Customizing & Memorizing Reports
- Open the report you want to customize
- Click "Customize Report" button
- On "Display" tab:
- - Change date range
- - Set report basis (Cash or Accrual)
- - Choose columns to display
- On "Filters" tab:
- - Filter by customer, vendor, account, class, etc.
- - Exclude zero-balance accounts
- On "Header/Footer" tab:
- - Add company name and logo
- - Customize report title
- Click "Memorize" to save custom report settings
- Access memorized reports under Reports → Memorized Reports
Share Reports with Your Accountant
Most accountants want to see: Profit & Loss, Balance Sheet, A/R Aging, and A/P Aging. Memorize these reports with "For Accountant" in the name so you can quickly generate them at tax time.
Best Practices for Small Businesses
Daily Habits
- • Record transactions same-day: Don't let receipts pile up
- • Check bank feeds: Match and categorize downloaded transactions
- • Follow up on overdue invoices: Send reminders promptly
Weekly Habits
- • Review Accounts Receivable Aging: Call customers with overdue invoices
- • Pay bills due this week: Avoid late fees
- • Review Profit & Loss for the week: Spot unusual expenses
Monthly Habits
- • Reconcile all bank and credit card accounts: Catch errors early
- • Review financial statements: P&L, Balance Sheet, Cash Flow
- • Back up company file: Save to external drive or cloud
- • Update customer/vendor information: Keep contact info current
- • Review unbilled time/expenses: Invoice all billable work
Quarterly Habits
- • Estimated tax payments: Pay federal and state quarterly taxes
- • Review budget vs. actual: Are you on track with financial goals?
- • Clean up chart of accounts: Merge or delete unused accounts
- • Meet with accountant/bookkeeper: Review reports and plan ahead
Annual Habits
- • Year-end close: Finalize all transactions for tax year
- • Generate 1099s for contractors: Due January 31
- • Provide W-2s to employees: Due January 31 (if using payroll)
- • Archive prior year: Create year-end backup
- • Plan next year: Create budget based on this year's performance
Common Mistakes to Avoid
❌ Mixing Personal and Business Expenses
Problem: Makes accounting messy, reduces tax deductions, creates legal liability issues
Solution: Open separate business bank account and credit card. NEVER mix funds.
❌ Not Backing Up Regularly
Problem: Hard drive failure = business data gone forever
Solution: Set up automatic daily backups to external drive AND cloud storage (Dropbox, OneDrive, etc.). Test restoring backups quarterly.
❌ Waiting Until Tax Time to Do Bookkeeping
Problem: Forgotten transactions, lost receipts, higher accountant fees, potential missed deductions
Solution: Record transactions weekly at minimum. Monthly reconciliation is non-negotiable.
❌ Not Reconciling Bank Accounts
Problem: Errors compound, financial reports are inaccurate, tax returns are wrong
Solution: Reconcile every account monthly. No exceptions.
❌ Using "Ask My Accountant" Account Too Much
Problem: Becomes a dumping ground for transactions you don't know how to categorize
Solution: Take time to learn proper categorization. Ask your accountant for guidance on setting up your chart of accounts.
❌ Not Saving Receipts
Problem: IRS audit = no receipts = denied deductions = owed taxes + penalties
Solution: Use QuickBooks receipt capture or scan/photograph receipts immediately. Save digitally for 7 years.
❌ Ignoring Cash Flow
Problem: Profitable on paper but can't make payroll = business failure
Solution: Run Cash Flow Statement monthly. Know what's coming in and going out. Build 3-6 month cash reserve.
❌ Not Following Up on Unpaid Invoices
Problem: Work done for free = lost revenue
Solution: Send invoice immediately after work. Follow up at 7 days, 14 days, 30 days. Friendly but persistent.
Frequently Asked Questions
Do I need QuickBooks if I'm a sole proprietor with simple finances?
If you have more than a handful of transactions per month, yes. Even simple businesses benefit from proper bookkeeping. QuickBooks makes tax time infinitely easier, and you'll catch deductions you'd otherwise miss. Alternative: QuickBooks Online Simple Start ($30/month) or Wave (free but limited).
Should I use cash basis or accrual accounting?
Cash basis: Record income when received, expenses when paid. Simpler. Good for small businesses with no inventory.
Accrual basis: Record income when earned, expenses when incurred. More accurate picture. Required if you have inventory or gross receipts over $25M. Most small businesses use cash basis.
Can I do my own bookkeeping or should I hire someone?
Do your own if: You have time, basic accounting knowledge, and fewer than 50 transactions/month.
Hire a bookkeeper if: You have more than 100 transactions/month, employees/payroll, inventory, or multiple revenue streams. Cost: $200-500/month depending on complexity. Consider it an investment in accuracy and your time.
How long should I keep QuickBooks records?
Tax documents: 7 years (IRS audit period)
Company files: Indefinitely (storage is cheap)
Receipts: 7 years digitally
Payroll records: 7 years
Best practice: Archive previous year's file annually but keep accessible.
What's the difference between QuickBooks Desktop and QuickBooks Online?
Desktop: Installed software, one-time purchase or annual license, more features, better for complex businesses, requires Windows
Online: Web-based, monthly subscription ($30-200/month), accessible anywhere, automatic updates, easier for beginners, better for simple businesses
Migration: You can convert Desktop → Online but not Online → Desktop
Can multiple people access QuickBooks Desktop at the same time?
Yes, with multi-user mode (requires Pro Plus or higher). The company file must be stored on a server or dedicated host computer. Each user needs their own license. Setup: File → Switch to Multi-user Mode. See our multi-user setup guide for detailed instructions.
How do I handle sales tax in QuickBooks?
1. Enable sales tax: Edit → Preferences → Sales Tax → Company Preferences → Yes
2. Add tax rates: Lists → Item List → Item → New → Sales Tax Item
3. Assign tax codes to customers (taxable/non-taxable)
4. Mark items as taxable or non-taxable
5. Run Sales Tax Liability report before filing
6. Pay sales tax: Vendors → Sales Tax → Pay Sales Tax
What if I made a mistake in a previous month/year?
Current year: Just fix it. Edit the transaction and reconcile again if needed.
Prior year (already filed taxes): Don't change! Create an adjusting journal entry in current year with explanation. Consult your accountant. Changing prior-year data can trigger amended tax returns.
Can I import data from Excel or another accounting system?
Yes. File → Utilities → Import → Excel Files. You can import customers, vendors, chart of accounts, and items. QuickBooks provides Excel templates. For full data migration from other software, use a data conversion service (Intuit offers this) or hire a QuickBooks ProAdvisor.
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