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Nonprofit audit accounting help, fast.

For nonprofits facing an audit with books that are behind, funds that are hard to trace, and a deadline that is not moving. We clean it up, prepare the file, and hand the auditors what they ask for.

What we do

Get you through the audit, and leave you with a finance function you can trust.

We specialize in nonprofit accounting for organizations with multiple funding streams, restricted funds, payroll complexities, and grant or union requirements. The goal is simple: clean books, clear documentation, and no scramble the next time an auditor asks a question.

01

Cleanup

Reconcile the accounts, correct the coding, and close the year properly. Whatever the last twelve months look like right now, this is the part that makes everything after it possible.

02

Audit preparation

Assemble the schedules, reconciliations and documentation the auditors are going to ask for, so requests come back in days instead of weeks and your staff keeps running the organization.

03

Ongoing outsourced finance department

Stay on after the audit closes as your accounting and finance function. Monthly close, payroll, grant reporting, and the controls that make the next audit routine.

We can come in as a short term audit rescue partner, or stay on as your ongoing outsourced accounting and finance department. Most organizations start with the first and decide about the second once the pressure is off.

Who it is for

Nonprofits between $2M and $100M in revenue, with an audit in front of them.

Big enough that the accounting is genuinely complicated, small enough that there is no full finance department absorbing it. That is the gap this service was built for.

This is you if

  • An audit is scheduled, or the board has just asked when the last one was
  • The books are behind, or nobody is confident they are right
  • Money arrives from several directions: grants, government contracts, contributions, program fees
  • Restricted funds live in a spreadsheet, or are not really tracked at all
  • Payroll spans multiple programs, grants, or a union agreement
  • The person who understood the accounting has left

What we do not do

  • Issue the audit opinion. That has to come from an independent audit firm, not from the people who prepared the books
  • Give legal opinions. Your attorney keeps that, and we route questions back
  • Argue with your auditor. We prepare the file, answer the requests, and document the positions we took

How it works

Four steps, and you know the cost before the work starts.

01Inquiry

  • Send the form at the bottom of this page
  • Tell us the size of the organization and the state you operate in
  • If the audit already has a date, say so, because it changes the order we work in

02Assessment call

  • A 45 to 60 minute conversation with our senior team
  • We look at where the books actually stand, not where they are supposed to be
  • We name what the auditors will need and what has to happen first

03Proposal

  • A written scope: what we clean up, what we prepare, and what it costs
  • Who does what on your side, so nothing sits waiting on an unnamed person
  • No open ended hourly arrangement you cannot put in front of a board

04Audit project, or ongoing support

  • A defined audit project that ends when the audit does
  • Or an ongoing outsourced accounting and finance department
  • You choose after the proposal, not before

Questions we get asked

Nonprofit audit preparation, answered plainly.

When should we start preparing for the audit?

As soon as the fiscal year closes, and earlier if the books are behind. Most of the pain in a nonprofit audit comes from rebuilding a year of records in the few weeks before fieldwork starts. If you already have a date, we work backwards from it.

Our books are months behind. Is it too late?

No. Catch up work is the most common reason organizations call us. We reconcile the accounts, correct the coding, and prioritize the areas the auditors will actually test, so the cleanest possible file is ready when fieldwork begins.

What will the auditors ask us for?

Usually a trial balance, reconciliations for every bank and investment account, contribution and grant documentation, restricted fund activity and release schedules, payroll records and allocations, board minutes, and support for significant journal entries. We assemble that package with you.

Can MSI also be our auditor?

No, and that is by design. Independence rules generally prevent the firm that audits you from also keeping your books. We work on your side of the table: we prepare the file and answer the auditors' questions so your staff is not buried in requests.

How do you handle restricted funds?

We track net assets with and without donor restrictions separately, document the restriction attached to each gift or grant, and keep release schedules current, so movement between the two is supported rather than reconstructed at year end.

We have grant reporting and union payroll. Do you cover that?

Yes. Multiple funding streams, cost allocations across programs and grants, union payroll and the reporting that comes with it are the conditions this service was built around. Organizations receiving federal funding may also face a Single Audit, which carries its own compliance testing.

Do we have to replace our bookkeeper or controller?

Not unless you want to. Plenty of organizations keep their internal team and bring us in for audit support only. Others hand us the whole function. Both are normal, and the assessment call is where we work out which one fits.

What happens once the audit is finished?

You decide. Some organizations take the cleaned up books and carry on from there. Others keep us on as their outsourced accounting and finance department, so the next audit is a scheduled event rather than an emergency.

Why MSI

Who you are actually handing the books to.

Two nonprofits we took from behind to audit ready, and the people who did it. Both organizations are described by sector rather than by name. Each one opens with what changed, and expands to the full account.

01

Children's suicide prevention nonprofit

Grew from roughly $200,000 to more than $25 million in annual revenue, with an accounting operation rebuilt to carry it.

Mission and fundraising had outrun the financial infrastructure behind them. MSI reconstructed the schedules, strengthened internal controls, and built procedures that scale, so the independent audits are now supported by organized records instead of a year end reconstruction.

  • Independent audits supported by organized records and significantly reduced follow-up
  • Established audit schedules and supporting documentation
  • Monthly financial reporting provided to the board
  • Organized support for millions of dollars in annual transactions
Read the full case studyHide the full case study

The challenge

A nonprofit organization experienced exceptional growth, expanding from approximately $200,000 in annual revenue to more than $25 million in a relatively short period.

The organization's mission and fundraising capabilities had grown far faster than the financial infrastructure behind them. Accounting systems and procedures had not been designed for an organization operating at this scale. Historical schedules were incomplete, supporting documentation was inconsistent, and financial activity was flowing through multiple outside partnerships and fundraising channels.

Leadership needed more than bookkeeping support. They needed a financial operation capable of supporting, protecting, and providing visibility into a multimillion dollar organization.

Our approach

MSI stepped in to help build the financial infrastructure the organization needed for its next stage of growth.

We reconstructed and standardized accounting schedules, reorganized financial records and supporting documentation, strengthened internal controls, and developed repeatable accounting procedures that could scale with the organization.

We also addressed historical and ongoing compliance matters, reconciled incomplete information received from outside partners, researched discrepancies, and developed reporting processes that gave leadership a much clearer understanding of the organization's financial position.

Rapid growth also meant leadership was regularly facing sophisticated financial questions without years of established accounting history or systems to rely upon. MSI became a resource for working through those questions, researching the underlying activity, reconstructing information when necessary, and building processes so the answers would be easier to obtain in the future.

Strengthening financial credibility

Our work extended beyond the internal accounting function.

We also helped strengthen the organization's external financial presentation, transparency, and overall financial credibility. Financial information was reviewed and organized to better support audits, board reporting, donor inquiries, outside partnerships, and the organization's public financial profile, including information considered by nonprofit rating organizations such as Charity Navigator.

As the accounting became more organized, consistent, and transparent, leadership was better equipped to clearly communicate the organization's financial story to donors, board members, auditors, partners, and the public.

The result

What began as an organization whose growth had outpaced its financial systems evolved into a more structured, controlled, and scalable accounting environment.

Today, the organization benefits from:

  • Consistent accounting procedures and documentation
  • Stronger internal financial controls
  • Organized support for millions of dollars in annual transactions
  • Monthly financial reporting provided to the board
  • Reliable financial information for management decision-making
  • Established audit schedules and supporting documentation
  • Ongoing financial oversight as new questions, challenges, and opportunities arise
  • Independent audits supported by organized records and significantly reduced follow-up

The organization can now operate at scale with financial systems designed not only to account for its growth, but to protect its mission, support its leadership, and strengthen the confidence of the donors and partners who make that mission possible.

Client rating for this engagement

02

Performing arts organization

Unreliable, incomplete records became a file the auditors could verify, prepared through the year instead of rebuilt at year end.

Turnover and inconsistent practice had left holes in the records, and entries had been used to force accounts into balance. MSI converted the organization from QuickBooks Desktop to QuickBooks Online, rebuilt the prior year from source documents, and now keeps the file audit ready year round.

  • Organized annual audits with substantially fewer questions, adjustments, and surprises
  • A clear audit trail from source documentation through the financial statements
  • Monthly financial statements and recurring reporting to the board
  • Consistent accounting schedules maintained throughout the year
Read the full case studyHide the full case study

The challenge

Fast moving nonprofits focused on their mission can develop significant financial complexity long before they have the internal resources and systems needed to manage it.

In this case, turnover among bookkeepers and directors, complex reporting requests from the board, combined with gaps in training and inconsistent accounting practices, had created substantial holes in the financial records. Historical information was incomplete, financial entries had been used to force accounts into balance, and auditors did not have a reliable trail to verify the prior year.

At the same time, management, the board, auditors, and outside stakeholders needed accurate financial information and dependable answers.

Our approach

MSI began by converting the organization from QuickBooks Desktop to QuickBooks Online so they could reconstruct the prior year outside of the active operating system.

Rather than simply carrying forward questionable historical balances, we worked through the accounting in detail, learning the organization's financial activity, identifying and removing errors, rebuilding missing information, and creating a financial file that could ultimately be supported and audited.

The work included:

  • Creating and maintaining detailed supporting schedules
  • Reconciling activity from outside partners and fundraising channels
  • Identifying missing financial information
  • Researching unexplained balances and discrepancies
  • Correcting unsupported or inaccurate accounting entries
  • Documenting unusual and complex transactions
  • Establishing procedures for recurring financial activity
  • Building a clear audit trail from source documentation through the financial statements

Where historical information was incomplete, MSI worked backward from available bank records, accounting records, partner reports, payment platform information, and other source documentation to reconstruct the financial picture.

Where processes were unclear or inconsistent, we created controls and repeatable procedures so the same problems would not have to be solved again.

Preparing for the audit before the audit begins

One of the most important changes was moving the organization away from a reactive year end audit process and into an audit ready accounting environment.

Supporting documentation, reconciliations, and financial schedules are now maintained throughout the year instead of being recreated only after auditors begin requesting information.

Complex transactions are researched and documented when they occur. Financial schedules are updated regularly. Discrepancies are investigated while the supporting information is still readily available.

This creates a clear trail from the financial statements back to the underlying transactions and supporting documentation.

It also means management can answer sophisticated financial questions throughout the year rather than waiting until year end to understand what happened.

Board and management reporting

Financial reporting was strengthened so management and the board could more clearly understand the organization's financial position and activity.

MSI developed recurring monthly reporting that gives leadership visibility into revenue, expenses, cash balances, significant financial activity, unusual transactions, and areas requiring attention.

Instead of accounting functioning simply as a historical record of what already happened, the financial information became a management tool that leadership could use to make decisions.

The result

The organization now operates with a significantly higher level of financial transparency, documentation, and control.

Improvements include:

  • Monthly financial statements and recurring reporting to the board
  • Detailed reconciliations supporting significant financial activity
  • Consistent accounting schedules maintained throughout the year
  • Documentation supporting transactions involving outside partners
  • Stronger controls over cash and financial reporting
  • Faster answers to complex financial questions
  • Greater transparency for donors and outside stakeholders
  • Better support for nonprofit ratings and publicly reported financial information
  • Organized annual audits with substantially fewer questions, adjustments, and surprises

Most importantly, leadership no longer has to choose between pursuing the organization's mission and understanding the finances supporting it.

The accounting operation has become part of the organization's infrastructure, supporting continued growth rather than becoming an obstacle created by it.

Client rating for this engagement

03

Who does the work

Nonprofit accounting sits inside the team. These are the specialties MSI already publishes on its own team page.

  • Julian Paiz, Senior Accountant. Non Profit Accounting, Excel, QuickBooks, Internal Controls, P&L Statements, Bank Account Audits, Third-Party Audits.
  • Maria Struve, Tax and Accounting Director. Two decades across public accounting, operations and wealth management.

Start here

Tell us where the audit stands.

We take on a limited number of audit projects at a time, so the ones we accept are properly staffed. The faster we see the situation, the more of it we can still fix before fieldwork.

Call or text(831) 220-3113
Where we areAlameda and Carmel, California

About the Nonprofit Audit FAQ

It is our own guide to how a nonprofit audit actually works: practical answers for nonprofit leaders, boards and finance teams. Submit the form and the download appears straight away. If the PDF is all you need for now, tick that box and say so.

Request an audit support call

Five fields and a few boxes. If your audit already has a date, tell us on the call and we work backwards from it.

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