Clean up your chart of accounts before you connect another system to Xero or MYOB, or move to a new one. Every integration maps its own codes onto your accounts, tracking categories or jobs, items, tax codes and contacts, so a messy chart gets copied into every system that touches it. The clean-up itself is straightforward: export the lists, find the accounts nobody uses or that duplicate each other, agree the reports you actually need, move the history into the accounts you're keeping, archive or make the rest inactive, and lock the periods you've finished with. Do it with your accountant, and do it before the mapping is built, not after.
Why a messy chart causes trouble once systems are connected
On its own, a cluttered chart is an annoyance the bookkeeper works around. Once another system is connected, every system gets its own copy of the mapping. Your job management system sends labour to one account, your inventory system posts cost of sales to another, and the expense app staff use picks from the full list and chooses whichever account looks right. Now the same cost lands in three places, each system's report is "right" by its own rules, and nobody's numbers agree. That is one of the common reasons systems give different numbers.
The same thing happens with the other lists an integration relies on:
- Tracking categories (Xero) or jobs and categories (MYOB): if one branch is called "Gold Coast", "GC" and "GC Branch", reports split three ways.
- Items: duplicate or retired item codes mean sales and stock post to the wrong income or cost account.
- Tax codes: a custom tax rate someone created years ago can be picked up by an integration and throw out the BAS.
- Contacts: duplicate customers and suppliers mean the integration matches an invoice to the wrong record, or creates a third one.
Fixing these after the integration is built means changing the mappings, re-testing and often correcting transactions that have already synced.
Step by step: cleaning up the chart of accounts
1. Export everything first
Export the chart of accounts, the trial balance for the current and last full financial year, tracking categories (or jobs and categories), items, tax rates and contact lists to Excel. This is your before picture. Our guide to getting data out of Xero and MYOB covers the exports.
Add two columns to the chart: each account's transaction count over the last two years (count lines in the general ledger report) and its balance.
2. Sort every account into keep, merge or retire
Go down the list and mark each account:
- Keep: used, clearly named, needed for a report someone reads.
- Merge: duplicates or near-duplicates, such as "Telephone" and "Phone & Internet", or one-off accounts set up for a single purchase.
- Retire: nothing posted for a year or more and no balance, or set up for something the business no longer does.
- Rename: the account is right but the name is vague ("Sundry", "Other Expenses 2") or doesn't match how people talk about it.
3. Decide what reporting you actually need
Before merging anything, write down the reports the owner, the bank and the accountant actually use: the profit and loss layout, gross margin by division or job, the balance sheet lines for the bank, and the BAS. Then ask of each account: does any of these reports need this account on its own, or could it be a line within a bigger account, or a tracking option?
This is where most charts go wrong: people add an account for every way they want to slice the numbers, such as "Wages - Brisbane", "Wages - Gold Coast" and "Wages - Sunshine Coast". Usually a single "Wages" account with a tracking category or job for the location is better.
4. Tracking categories or separate accounts?
A simple rule of thumb: use accounts for what the money is (wages, materials, freight, rent) and tracking categories or jobs for where or who it belongs to (branch, division, project, job).
In Xero you only get two active tracking categories, so pick them carefully. If you need to report by more than two things, see our post on what to do when two tracking categories isn't enough. MYOB AccountRight uses jobs and categories for the same purpose, and the same rule applies.
Agree the list of tracking options at the same time. Every option should have one spelling, and old branches or finished projects should be archived, not left active for people to pick.
5. Move the history, then archive or make inactive
What each system allows (as at October 2026, from Xero and MYOB help pages and their product forums):
- Xero doesn't have a merge accounts feature, and Xero has said on its product ideas board that it isn't in its plans. You can delete an account that has no transactions. An account with history can be archived instead. To bring two accounts together, an adviser user can use Find and recode to move the transactions from one account to the other, then archive the empty one. Accounts used in an active bank rule or repeating transaction can't be archived until you change those, and system accounts (shown with a padlock) can't be removed.
- MYOB AccountRight has a Combine accounts feature: the transactions and opening balance of the secondary account move into the primary account and the secondary account is removed. The accounts must be the same type, accounts linked to a job can't be combined, and it can't be undone, so take a backup first. Unused accounts can be made inactive so they stop appearing in lists.
- MYOB Business (browser): MYOB's community forum says combining accounts is only available in the desktop AccountRight software. Check MYOB's current help before you rely on this, as features change. If combining isn't available, moving balances with a journal and making the old account inactive is the usual approach; agree that with your accountant, because a journal moves the balance but not the transaction history.
Whichever system you use, recoding or combining changes historical reports, including periods your accountant may already have reported on. Talk to them before you touch anything before the last lodged BAS or the last finalised year.
6. Use a naming and numbering convention
Pick a pattern and stick to it, for example:
- Number ranges by type (income in the 4000s, cost of sales in the 5000s, expenses in the 6000s), with gaps left so new accounts fit in the right place.
- Names that say what the account is, without abbreviations only one person understands.
- No locations, years or people's names in account names. Those belong in tracking or jobs.
Write it down so the next person follows it.
Then do the same for items, tax codes and contacts
The chart is the big one, but integrations lean on these lists just as heavily:
- Items: retire codes you no longer sell or buy, fix any item pointing at the wrong sales or purchase account, and make sure each item has the right tax code.
- Tax codes: remove or deactivate custom tax rates that duplicate the standard GST ones. Each integration should map to a small set of tax codes your accountant has agreed.
- Contacts: merge duplicate customers and suppliers. Xero can merge contacts and AccountRight can combine cards, both keeping the history. Our post on cleaning up duplicate records before a migration covers how to find them.
Lock the clean-up in place
When the clean-up is done and the accountant has checked the trial balance against your before picture, set a lock date so nobody, including a newly connected app, can post into finished periods:
- Xero: under Financial settings, set the lock date. One setting stops everyone except advisers; the other stops everyone, advisers included.
- MYOB AccountRight: Setup, Preferences, Security tab, then lock periods up to and including a date.
- MYOB Business: a lock date is set in your business settings.
Integrations generally can't write into a locked period, so a sync error after go-live may just mean a transaction is dated too far back.
Finally, limit who can add new accounts and tax codes, so the chart stays clean.
When it's worth getting help
Many businesses can do this themselves with their bookkeeper and accountant over a few sessions, especially with a single company and one or two connected apps. It's worth getting help when:
- several companies need the same chart so you can consolidate them;
- you're about to connect a job system, inventory system or CRM and need the mapping designed at the same time;
- you're moving to a new system and the clean-up is part of the migration;
- years of history need recoding and you want it checked against the original reports.
Our accounting data migration service covers clean-ups done as part of a move, and our Xero and MYOB integration and migration guide brings the related articles together. If you're not sure what needs fixing first, our $5,000 Process & Systems Audit maps your systems and how data moves between them, and gives you a written report.
Frequently asked questions
Can you merge accounts in Xero?
Not directly. Xero has no merge accounts feature. An adviser user can use Find and recode to move transactions from one account to another, then archive the empty account. Check with your accountant first, because it changes historical reports.
How do I combine accounts in MYOB?
In MYOB AccountRight, use the Combine accounts feature from the Accounts List. Both accounts must be the same type, accounts linked to a job can't be combined, and it can't be undone, so back up first. According to MYOB's community forum, combining isn't available in the browser-based MYOB Business.
Should I use tracking categories or more accounts?
Use accounts for what the money is and tracking categories (or jobs in MYOB) for where it belongs, such as a branch, division or project. Adding an account for every location makes the chart grow every time the business changes, and every connected system then needs updating.
Should I clean up the chart of accounts before or after migrating?
Before, wherever you can. Mapping a clean chart is far simpler than fixing a messy one later, and your accountant can check the trial balance before and after while the old system is still running.
If you'd like to talk through your chart of accounts before connecting or moving systems, book a free initial chat.