SMSF Audit Checklist for Accountants

An SMSF audit file needs the fund’s governing documents, reconciled accounts and evidence for its investments and member transactions. Send one indexed package to the appointed auditor. Complete the audit and obtain the auditor’s report before lodging the SMSF annual return.

Assembling the Audit File for the Auditor

Group the audit pack by document type, with each account balance linked to its supporting records. Use this checklist as the starting index, then add the appointed auditor’s fund-specific requests.

File group	Documents to include	Preparation check
Governing documents	Executed deed, every variation, trustee appointment records, trustee declarations, member applications and investment strategy	Confirm the documents cover the trustees and members during the audit year. Include strategy reviews and the trustees’ consideration of insurance.
Trustee decisions	Minutes and resolutions for investment decisions, contributions, pensions, benefits and changes to trustees	Link each decision to the transaction or member record it supports.
Banking	Full-year statements for every account, term-deposit records and reconciliations	Account for opening balances, closing balances and transfers between fund accounts.
Investments	Holdings statements, purchase and sale records, income statements and ownership evidence	Reconcile quantities, income and year-end market values to the accounts.
Contributions	Receipt details by member, employer and personal contribution records, deduction notices and acknowledgements where relevant	Match each receipt to its contribution type and the member’s records.
Benefits and pensions	Pension commencement documents, condition-of-release evidence, minimum-payment calculations and payment records	Reconcile pension payments separately from lump sums and commutations.
Year-end accounts	Draft financial statements, trial balance, general ledger, tax calculation and member statements	Clear suspense balances and explain adjustments before sending the file.
Fund-specific records	Rental leases and statements, property expenses, related-party agreements and limited recourse borrowing documents	Include loan statements, repayment records, holding-trust documents and evidence of transaction terms where applicable.

The ATO’s approved SMSF auditor checklist connects supporting records to financial and compliance checks. Contributions need acceptance evidence. Benefits need payment-standard evidence. Income and deductions need source documents. An investment strategy alone cannot prove that transactions meet the fund’s obligations.

For crypto, include evidence that the fund owns the exchange account and has a separate wallet from the trustees’ personal holdings. Supply transaction histories and transfer records. Reconcile units and dollar values to the accounts, including year-end exchange-price evidence. Keep credentials and private wallet keys out of the pack. The ATO explains these requirements in its SMSF investment guidance.

Check GST on audit fees against the invoice and the fund’s circumstances. A fund without GST registration cannot claim an input tax credit. Registration alone does not establish a full credit either. Assess the acquisition’s purpose and any apportionment under the GST rules.

The ATO’s reduced credit acquisition ruling excludes taxation and auditing services from item 24(h). Do not automatically apply a reduced credit to a standalone audit invoice. Record the basis for any credit separately from the income-tax deduction.

Send the pack through secure file sharing with a numbered index and version identifier. Mark irrelevant items as not applicable with a reason. List missing items with an owner and expected delivery time, so the auditor can identify an incomplete file immediately.

Confirm the Auditor Before the File Goes

Record the appointed auditor’s confirmed details before arranging the annual file handover. Keep the auditor’s name, SMSF auditor number, contact details and agreed delivery channel in the fund’s annual file.

The trustees must appoint the auditor no later than 45 days before the annual return is due. If the auditor requests relevant documents in writing, the trustees must provide them within 14 days of the request. The ATO’s auditor responsibilities guidance also gives the auditor 28 days after receiving all relevant documents to provide the report.

Agree who answers queries and who can obtain documents from trustees. Confirm the auditor has received the package and can open it. If appointment checks remain unfinished, use the separate guide to choosing an SMSF auditor before this handover.

Year-End Valuations and Member Records

Support each year-end asset value with objective evidence that fits the asset and the valuation point. Trustees must value fund assets at market value when preparing annual accounts. Retain the method and evidence beside the reported value.

Asset	Evidence to assemble
Listed shares and units	Year-end holding quantities and published market prices, reconciled to broker or registry statements.
Real property	A reasoned assessment supported by comparable sales or an appropriate valuation report. Explain changes in the property or market since an earlier assessment.
Unlisted investments	Financial information about the underlying entity, its assets and liabilities, plus a supported valuation method. A balance copied from the previous year is insufficient by itself.
Collectables	Evidence supporting market value, with ownership, storage decisions and insurance records. A transfer to a related party requires a qualified independent valuer.

Use the ATO’s valuation guidelines for the applicable evidence standard. A professional property valuation is not automatically required every year. An old report still needs evidence that the value remains appropriate. The auditor decides whether the supplied evidence supports the accounts.

Reconcile each member’s opening balance to the previous signed accounts. Trace contributions, rollovers, allocated earnings, expenses and benefit payments through to the closing balance. Compare contribution records with the member’s applicable caps and any relevant contributions to other funds.

Keep pension commencement and commutation records with transfer balance account reports and their receipts. Reconcile pension payments to the calculated minimum for each applicable pension. Obtain the actuarial certificate where the fund’s exempt current pension income calculation requires one. Paying a pension does not make a certificate compulsory in every case.

Treat unsupported property values and missing required actuarial certificates as pre-handover exceptions. Assign someone to resolve them before promising a complete pack.

How the Audit Fits With the SMSF Annual Return

Prepare the accounts, complete the audit and obtain the independent auditor’s report before lodging the SMSF annual return. The annual return records the auditor’s details and audit information. Use the final report to complete those fields.

1. Finish the draft accounts and member reconciliations, with supporting documents indexed.
2. Send the complete file to the appointed auditor and answer written queries.
3. Review the signed auditor’s report and management letter with the trustees. Update the accounts or return where a correction is required.
4. Obtain the trustees’ authorisation for the return and lodge it with the correct audit details. Retain the report and lodgment receipt together.

A newly registered fund and an established tax-agent client can have different deadlines. An earlier deadline can also follow a registration review or overdue returns. Use the fund’s recorded ATO due date and the ATO’s super fund lodgment program to set the handover schedule. Allow time for queries before the return is due. The tax agent lodgment program guide explains how agent-program eligibility affects scheduling.

An auditor contravention report is separate from the report sent to trustees. The auditor applies the ATO’s contravention reporting tests. These cover the fund definition, new-fund circumstances, trustee behaviour and financial thresholds. The auditor can also report other concerns using professional judgement.

Discuss the breach, its effect on the accounts or return and the trustees’ rectification actions. Preserve supporting records and correspondence. Rectifying an issue does not automatically remove the auditor’s reporting obligation. A report can lead to ATO review or compliance action, but reporting alone does not decide that the fund is non-complying.

Queries That Hold Up SMSF Audits

Answer likely audit queries with a document reference and a short explanation before sending the pack. Use a query log for matters that need a decision or additional evidence.

Likely query	What to put in the file
Missing bank statements	A full-year statement range for every account, including accounts closed during the year. Explain any unavailable period and obtain replacement records.
Unexplained transfers	The source and destination account references, transaction purpose and member allocation where relevant. Match both sides of a fund-to-fund-account transfer.
In-house assets	A related-party schedule, valuation support and the applicable limit calculation. Explain any exception being relied on and include a required reduction plan.
Unclear asset ownership	Title, registry or custody evidence showing the trustees hold the asset for the fund. Explain legally recognised holding arrangements, including a holding trust where applicable.
Loans to members	Full transaction details and trustee correspondence. Escalate the breach for rectification instead of treating a repayment as proof that the original loan was permitted.

The ATO’s investment restrictions prohibit loans or financial assistance to members or their relatives. The in-house asset rules have a separate 5% limit and specific exceptions. Do not treat that limit as permission to lend to a member.

In the log, record the question, document reference, responsible person, response and closure status. Carry unresolved matters and recurring missing documents into the next year’s collection checklist.

Speeding Up Audit Turnaround, Including With AI

Shorten audit turnaround by collecting evidence during the year and clearing reconciliation differences before handover. Bank data feeds help prepare accounts, while statements remain part of the evidence pack. Monitor feed gaps and duplicate transactions.

Set a standard index for the practice and agree a delivery deadline for each fund. Request documents when trustees buy an asset, start a pension or enter a related-party arrangement. Those records are easier to collect at the event than after year-end.

AI can assist with a statement summary, proposed transaction matches or a draft query list. A staff member must check the result against the original records. Retain source references so the auditor can follow the transaction without relying on an AI summary.

The TPB’s AI guidance keeps responsibility for tax services with the practitioner. Before disclosing client information to a third-party AI tool, obtain permission unless a legal duty permits disclosure. Review how the tool stores and uses information. Do not upload fund records to a tool that fails the practice’s confidentiality requirements. The broader guide to AI for accountants covers that assessment.

Setting Up the Audit Workflow When You Take on a Fund

Start a transferred fund’s audit file with the previous reports and opening-balance evidence. Obtain the last independent auditor’s report and management letter, any contravention reports, previous annual returns and the auditor’s contact details.

Collect the signed prior accounts, member balances and investment records that support the opening position. Review outstanding audit queries and trustee rectification commitments. Confirm the appointed auditor’s contact and file-delivery arrangements before assembling the first annual pack.

Use the practice’s onboarding form to request the deed and variations, trustee records, investment strategy and documents for the fund’s actual holdings. The SMSF establishment checklist helps identify original fund records that must accompany the handover.

Tax Genie lets your practice build a fund-specific document request and automatically reminds trustees about outstanding items. Trustees upload documents through the client portal, and staff see each item’s owner and progress. Use that collection record to identify gaps before preparing the auditor’s package.

Before release, have the preparer compare the index with the accounts and the auditor’s request list. Every applicable item must have a document reference or an explained exception. Record the package version, recipient and receipt confirmation, then keep the query log with the fund’s annual file.