What’s the Best Accounting Software for My Business?

(When reconciliation is a must — and why QuickBooks Online & Wave stand out)

One of the most frustrating financial tasks for a small business owner is trying to align your bank statements with your books at month’s end. If your accounting software doesn’t let you reconcile right inside the program, you’re almost guaranteed to waste time exporting, comparing, and cross-checking in spreadsheets.

“If you are using a bookkeeping software that you can’t reconcile within the software, you need to change the bookkeeping software.” Melanie Queen

So, if reconciliation is non-negotiable for you, here’s a guide to choosing—and making the most of—an accounting platform that keeps your books clean,

compliant, and stress-free.

Why Reconciliation Matters (Beyond Just Clean Books)

Before we dive into software comparisons, let’s review why reconciliation is such a critical feature—especially from a tax and compliance standpoint.

1. Ensures Accuracy & Detects Errors

Reconciling your bank and credit card accounts helps you catch mistakes, missing entries, duplicate charges, or fraud. It’s your month-end integrity check.

2. Supports Reliable Reporting & Decision-Making

If your books are reconciled, your profit & loss, cash flow, and balance sheet reports will reflect reality. That makes your business decisions more trustworthy.

3. Helps in Audits & IRS Examinations

If the IRS audits your business, they often ask for your backup accounting files—not just PDF reports. According to the IRS, when you use electronic accounting software, they may request your administrator’s credentials and full backup of the data file to review. They expect that electronic systems provide a complete and accurate record of your data, and that your system should allow for retrieval, indexing, and reproduction of records.

In short: reconciliation is more than bookkeeping hygiene—it’s part of keeping your books defensible.

4. Meets IRS Recordkeeping Standards

The IRS allows you to choose whichever recordkeeping system you like (manual or electronic), as long as it “clearly shows income and expenses” and is backed by supporting documentation (receipts, canceled checks, deposit slips, etc.). When you use an electronic accounting system, all the same standards (accuracy, accessibility, audit trail) apply.

What Melanie Queen Says About QuickBooks & Wave

Melanie Queen offers a practical, grounded perspective from the trenches of small business bookkeeping. In her post Learn the Basics of Bookkeeping, she notes:

• QuickBooks remembers frequent transactions by vendor, reducing how much you manually recategorize.

• Wave does let you reconcile, but lacks the intelligent automation and reporting depth of QuickBooks.

• In Which Online Bookkeeping Is Best for You? She emphasizes that both QuickBooks Online and Wave use double-entry accounting and support reconciliation—unlike some competing platforms.

• QuickBooks has more built-in AI features, reporting, and scalability. Wave may work fine for a simpler or newer business, but if you outgrow it, transitioning becomes harder.

  
  

QuickBooks Online vs. Wave: Feature-by-Feature for Reconciliation & Beyond

Here’s a comparative breakdown you can use (or present in your blog) to help your readers—or yourself—choose wisely.

Feature / Criterion	QuickBooks Online	Wave
Reconciliation Workflow	Robust, built-in reconciliation module; auto-match suggestions, adjustment entries, and discrepancy resolution.	Supports reconciliation via its Accounting → Reconciliation tool.
Automated Bank Feeds & Matching	Connects to many banks; supports rules, memorization, and some AI matching logic	Supports bank connections; matching and categorization are more manual and less “learning”
Reporting & Analytics	Rich, flexible reports out-of-the-box (compare months/years, variance, forecasts)	Basic reporting; more manual effort required for comparative or custom reports (e.g. export to sheets)
Scalability & Upgrades	Multiple tiers, add-ons, users, advanced modules (e.g. inventory, projects)	More limited; may force you to switch software once your needs exceed what Wave offers
Cost	Subscription-based (varies by plan, users, features)	Core accounting features are free; you pay for extra services (e.g. bank connection, payroll, and payments)
Learning Curve / Ease of Use	More features = slightly steeper ramp, but many guides / support available	Simpler interface, but fewer automations mean more manual work
Audit / Backup & Export	Strong backup, export, audit trails; widely known and trusted by accountants	Has export features, but may have fewer audit-grade controls
Community / Support	Broad ecosystem, many third-party integrations, deep support	Smaller support pool; less depth in third-party integrations

Bottom line: QuickBooks Online gives you more “guard rails” to make reconciliation easier and more automatic. Wave does work (especially early on), but you trade off convenience, speed, and growth potential.

Other Alternatives (Worth Mentioning)

Even though my preference leans toward QuickBooks or Wave, it’s good to know what else is out there—especially if your business has special needs.

• Xero — Strong in cloud accounting, good reconciliation workflows, many integrations. But my concern is how some versions of Xero handle matching (she asserts that reconciliation must be a full two-way check and not just accepting transations.

• Zoho Books — A middle ground: decent automation, good integrations, a strong value for growing businesses.

• FreshBooks — Great for service businesses or freelancers, though its reconciliation capabilities are more limited.

• Industry-specific platforms — If you’re in retail, manufacturing, nonprofits, etc., specialized systems may offer reconciliation plus domain-specific workflows.

  
  

Whenever you evaluate a new option, test how reconciliation works in that platform. Can you:

1. Enter or import a bank statement?

2. Match or suggest matches for entries?

3. Mark differences or adjustments?

4. Generate a reconciliation report that shows cleared vs outstanding items?

5. Handle leftover discrepancies or “unreconciled” items?

If any of those steps is clunky, that’s a red flag.

Tips for Making Reconciliations Smooth & Habitual

• Reconcile monthly (or more often). Don’t let transactions pile up.

• Use rules and automation (in QuickBooks especially) to auto-classify recurring transactions.

• Always include supporting documentation (receipts, invoices, statements) tied to entries.

• Maintain a good audit trail (don’t delete entries silently) so you can track adjustments.

• Export and back up data regularly—especially since the IRS may request your software file in an audit.