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An organization needs to have reliable financial systems. I use ADP for payroll and Quickbooks Online ($75/year from Quickbooks.) Quickbooks works up to about $2M-$3M in annual revenue.
There needs to be someone that really understands accounting (either staff or consultant). This means a lot more than writing checks. It means understanding accrual accounting.
It means a major commitment of time from ALL staff. Time sheets need to be prepared timely and accurately – no catching up at the end of the year. All expenses need documentation and allocation -timely, not when one feels like it.
In my nonprofits, I scan copies of all documents and attach that documentation to each transaction in in Quick. If a deposit is entered, attached is a copy of the check and the deposit ticket in Quickbooks. If a bill is paid, I include a copy of the invoice – if approved by email, a copy of the email is attached as well.
This makes audits so much easier. The documents are right with the transactions.