Year-End Bookkeeping Checklist for Multi-Entity Owners

For owners running multiple LLCs, year end is not one project — it's the same project run in parallel across every entity, plus a consolidation layer on top. Done well, your CPA receives a CPA-ready package per entity and the year-end conversation is about tax strategy, not data cleanup. Done badly, January and February disappear into corrections.

This is the checklist we run with multi-entity owners every December and January.

1. Reconcile every account in every entity

Every bank account, credit card, merchant account, and loan in every LLC reconciled through December 31. Any reconciliation discrepancies investigated and cleared — not parked in an undeposited funds or suspense account.

2. Clean up intercompany activity

Intercompany loans, transfers, owner contributions, and distributions reviewed and reconciled symmetrically across entities. "Due to / Due from" accounts should net to zero across the group at year end. Untangling intercompany activity at the CPA's hourly rate is one of the most expensive things you can do.

3. Fixed assets and depreciation

Fixed asset additions and disposals captured per entity for the year. Depreciation schedules updated by your CPA flow back into each entity's books. Confirm large purchases above your capitalization threshold weren't expensed to repairs and maintenance by mistake.

4. 1099 prep across all entities

Every entity that paid a 1099-eligible vendor needs the same hygiene: W-9 on file, vendor flagged as 1099-tracked in QBO, payments coded to a dedicated expense account. Run the 1099 detail report per entity in early January and reconcile to vendor ledgers.

5. Payroll, retirement, and benefits tie-out

Payroll totals from your payroll provider (Gusto, ADP, Rippling, OnPay) tied to the wage and payroll tax accounts in each entity's QBO file. Retirement contributions, HSA contributions, and owner health insurance verified and coded correctly.

6. Owner activity, separated cleanly

Owner draws, distributions, capital contributions, and personal expenses run through the business identified and reclassified. The cleaner the owner-versus-entity separation, the easier the CPA's allocation work.

7. Consolidated reporting package

Consolidated trial balance, P&L, and balance sheet across all entities with eliminations applied. This is the document that lets you (and your CPA) see the whole picture in one place — and it's the one most multi-entity owners are missing.

8. CPA-ready year-end package

Per entity: trial balance, GL detail, fixed asset schedule, loan schedules with year-end balances, payroll reports, 1099 detail report, copies of W-9s, and a brief year-end memo flagging anything unusual. Delivered to your CPA in the first two weeks of January.