Can you recommend bookkeeping software for cleanup and catch-up bookkeeping with client-specific chart of accounts?

Yes — for cleanup and catch-up bookkeeping with a client-specific chart of accounts (COA), you’ll usually want software that supports:

• Custom chart of accounts per client
• Bulk transaction editing/import
• Bank feeds + rule automation
• Audit trail / change tracking
• Multi-client management if you’re doing this for multiple businesses
• Strong accountant/bookkeeper workflows for reconciliation and historical cleanup

Best options

1) QuickBooks Online Accountant

Best overall for bookkeeping firms

• Supports custom COA per client
• Strong for catch-up work, bank feeds, and reconciliations
• Good accountant tools for switching between clients
• Widely supported by CPAs and bookkeepers
• Works well if you need to standardize cleanup processes

Downside: Can get messy if clients’ books are very disorganized, and bulk cleanup can still be tedious.

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2) Xero

Best for cleaner workflows and flexibility

• Fully customizable COA
• Good bank reconciliation and transaction matching
• Cleaner interface than QuickBooks for many users
• Good third-party app ecosystem
• Solid for multi-client bookkeeping practices

Downside: Some accountant-specific features and U.S. support/accounting workflows may feel less deep than QuickBooks depending on your needs.

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3) Sage Intacct

Best for more complex or growing clients

• Highly customizable COA and dimensions
• Strong reporting and controls
• Better for clients with multiple entities, departments, or advanced needs

Downside: Usually overkill and more expensive for small cleanup/catch-up work.

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4) Wave

Best for very small clients / lightweight cleanup

• Simple COA setup
• Basic bookkeeping and categorization
• Low cost

Downside: Not ideal for serious cleanup work or accounting firms managing many clients.

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5) Zoho Books

Best value option

• Custom COA
• Good automation and rules
• Decent for bookkeeping cleanup on smaller businesses
• Lower cost than QBO/Xero in many cases

Downside: Less common in CPA/bookkeeping workflows, so client/accountant familiarity may be lower.

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If your main need is cleanup/catch-up bookkeeping

I’d narrow it to:

1. QuickBooks Online Accountant — if you want the most standard, easiest-to-hand-off option
2. Xero — if you want a cleaner user experience and strong reconciliation
3. Zoho Books — if budget matters and clients are smaller

Important note

If by “client-specific chart of accounts” you mean:

• each client has a different COA, that’s normal in all of the above
• you need one platform to manage many clients with templated COAs, then QuickBooks Online Accountant or Xero practice tools are usually the best fit

My practical recommendation

• For a bookkeeping firm: QuickBooks Online Accountant
• For a tech-forward practice: Xero
• For budget-conscious small clients: Zoho Books

If you want, I can also give you a side-by-side comparison table of these tools specifically for catch-up bookkeeping, cleanup, and multi-client workflows.