Moving your books from one accounting system to another is one of those projects that looks like a weekend job and turns into a month. The software part is easy. The hard part is everything living inside your current file: three years of invoices, a vendor list nobody has cleaned since 2022, bank reconciliations, sales tax filings, and a chart of accounts that grew by accident.
Done badly, an accounting software migration leaves you with duplicate transactions, opening balances that don’t match your last tax return, and a trial balance that never quite ties out again. Done well, you close one system on a clean date and open the next one with numbers you can defend to your CPA. This guide covers how to get the second outcome.
Key Takeaways
- Clean and reconcile the old system before you export anything. Whatever mess you carry over becomes permanent.
- Pick a cutover date at a period boundary, ideally the first day of a quarter or your fiscal year.
- Export the full report set and the core lists, then keep both systems running side by side for at least one month.
- Compare the trial balance account by account, not just net income.
- Keep read-only access to the old software for a full tax cycle.
Step 1: Take inventory of what your current system holds
Before you move anything, write down what is actually in there. Your data sits in three layers. At the top are the summary financials. In the middle are the transactions themselves. At the bottom sit the supporting documents: receipts, bank statements, and attachments.
Export the customer and vendor lists, every invoice and bill, expense records, bank transaction history, tax returns, and any payroll reports if you run payroll through the same system. Save each export as CSV, and save the reports as PDF too. Put copies in two places, one local and one in cloud storage.
These exports are your evidence. Six weeks from now, when the new system shows a checking balance that is $412 off, you’ll want to know exactly what the old system said on the day you left it.
Step 2: Clean up the old books first
The new platform will faithfully reproduce whatever you feed it, including the problems. So fix the problems on the old side, where you already know where everything lives.
Reconcile every bank and credit card account through your planned cutover date. Look at undeposited funds and clear payments that have been sitting unapplied for months. Write off invoices you’ll never collect. Void checks that never cleared. If accounts receivable or accounts payable show a negative balance for any customer or vendor, find out why and correct it now.
You are aiming for a closed period with no loose ends. When you get there, run a final balance sheet and trial balance, save both as PDF, and treat them as the starting line for everything that follows.
Step 3: Choose the cutover date carefully
This is where most migrations go sideways. Someone signs up for new software on a random Tuesday, connects the bank feed, imports a few months of transactions, and then can’t explain why revenue doubled in the reports.
The cleanest cutover dates are January 1, the first day of a fiscal quarter, or the first day of any month where the books are fully reconciled. Avoid switching in the middle of a month, in the weeks before a tax deadline, or while your accountant is buried in year-end work.
Plan for two to four weeks of overlap where you can still log into both systems. That window is what lets you verify the imported numbers against the originals before you commit.
Step 4: Pick software that fits how you actually work
Choosing the replacement is the biggest decision in the whole process, and it deserves more than a feature checklist. Think about the three or four tasks you do every week and confirm the new system handles them without workarounds. For most small businesses that means bank feeds, invoicing, paying bills, categorizing expenses, and pulling a profit and loss at month end.
Ask how the software imports lists and opening balances, what file formats it accepts, and whether the reports it produces line up with the ones you’re used to reading. If you’re leaving a desktop product, check that the new tool can handle your data structure without you rebuilding it by hand.
This is the situation GlassJar was designed around. Every transaction and journal entry is entered from a single screen, bank feeds connect directly, and the customizable report library lets you build a trial balance or P&L that matches the layout you were using before, which makes the parallel-run comparison in Step 7 a lot less painful. Early access opens October 1, 2026, with a 14-day free trial.
Step 5: Export the full report set and the core lists
At minimum, export these reports before you begin: balance sheet, trial balance, profit and loss for the current year through the cutover date, profit and loss for the prior year, general ledger detail, accounts receivable aging, and accounts payable aging.
Then the lists: chart of accounts, customers, vendors, employees, products and services, and any class, department, or location structure you use for tracking. Finally, pull bank and credit card statements through the cutover date so you have third-party confirmation of every balance.
Create a folder with subfolders for reports, lists, statements, tax documents, and attachments. It feels like busywork. It saves hours the first time an auditor or lender asks for something from the old system.
Step 6: Import into the new system and check the opening balances
Most modern accounting platforms accept CSV imports for contacts, invoices, and the chart of accounts. Follow the new system’s own import format rather than inventing your own, because column mapping is where most import errors are born.
Once the data is in, check the opening balances against the reports you saved in Step 5. Focus on the figures most likely to drift: open invoices, unpaid bills, and bank balances. If one of those is off, stop and fix it before you enter a single new transaction.
Connect your bank accounts early so live transactions start flowing. That gives you a second source of truth to reconcile against while you are still inside the overlap window.
Step 7: Run both systems in parallel for a month
For at least one full close, keep entering transactions in both systems and compare the output. Trial balance, balance sheet, profit and loss, bank reconciliation, AR aging, AP aging. Every one of them, old versus new.
Don’t stop at net income. Net income can match while the balance sheet is wrong. Go through the trial balance one account at a time. When you find a difference, sort it into one of five buckets: a timing difference, a duplicate transaction, a missing entry, a wrong opening balance, or a mapping error. Each bucket has a different fix, and naming the bucket usually points straight at the cause.
Nearly every difference is fixable. The point of the parallel run is to find them while the old system is still there to check against.
Step 8: Archive the old system, don’t cancel it yet
Once the new system is your book of record, resist the urge to cancel the old subscription the same week. You may still need it for an audit, a prior-year amended return, a customer payment dispute, a vendor credit from last spring, or an insurance claim.
Keep read-only access for at least one full tax filing cycle. Many vendors offer a cheaper view-only tier for exactly this purpose. If your CPA asks for the detail behind a transaction from eight months ago, you want to open it, not reconstruct it from a folder of PDFs.
What should you actually bring over?
Not everything needs to make the trip. Decide which layers belong in the new platform and which can stay archived.
For most small businesses the list looks like this: current-year transaction detail, prior-year trial balance, open receivables, open payables, bank and credit card balances as of the cutover date, customer and vendor lists, the chart of accounts, and the products or services you invoice for.
If the old file is clean and the new platform can import detailed history, bring the history. You get trend reporting and year-over-year comparisons right away. If the old file is a mess of bad categories, bring clean opening balances only and keep the old software as a locked archive. Importing years of miscoded transactions just moves the mess to a new address.
How long does an accounting system migration take?
It depends on size and complexity more than anything. A freelancer with two years of invoices can finish in an afternoon. A small business with several bank accounts, inventory, and payroll should plan on two to four weeks of active work.
Add a month for the parallel run. After that, keep the old system reachable for another three to six months for lookups and tax questions. A migration that takes an extra week is cheaper than one that creates six months of cleanup.
Where GlassJar fits
GlassJar was designed for small businesses that want accounting software they can run without a workaround for every task. The contact management model lets one record act as both a customer and a vendor, so you aren’t importing the same company twice. Bank feeds connect directly, invoicing and bill management are built in, and the report library is customizable, which is what makes the parallel-run comparison in Step 7 workable.
Live chat support is available on every plan (Foundation, Core, and Advanced), and you can try it free for 14 days once early access opens October 1, 2026. Details are on the pricing page.
Frequently asked questions
Can I migrate accounting software without hiring someone?
Usually, yes. Most small business owners can handle it with good preparation: clean the old file, pick a period-boundary cutover date, and run both systems in parallel for a month. Bring in a bookkeeper if your old file has years of unreconciled accounts, because cleanup is where the real time goes.
What if something goes wrong during the import?
If you saved the full report set and list exports before starting, you can delete the bad import and load the clean CSV files again. Check opening balances against your saved trial balance before you go further.
How do I handle open invoices when I switch?
Export the accounts receivable aging report as of the cutover date and bring those open invoices into the new system as opening receivables. That way, when customers pay, you record the payment against the right invoice instead of an unexplained deposit.
Should I migrate all historical transactions or just opening balances?
If the history is accurate, bring it, because you get comparative reporting immediately. If the history is messy, bring opening balances only and keep the old system as an archive. There is no prize for importing bad data.
When is the safest time to switch?
The first day of your fiscal year is best, followed by the first day of a quarter. Books are reconciled, year-end reports are done, and you start clean. Avoid the middle of a month and the weeks before a filing deadline.
How do I know the migration worked?
Compare the trial balance in the new system to the final trial balance from the old one. Every account should match. Then run a bank reconciliation in the new system starting from your last reconciled statement. If both come out clean, you’re done.
