Finance & Accounting System

How to Pick the Right Accounting System for My Non-profit?

When an organization is formed and begins to take shape, one of the most important disciplines to pick the right accounting system for non-profit or for-profit organizations. Some can argue that you need an accounting system and not a financial system or vice versa. But the truth it, you just need to start somewhere so you have a place to grow from instead of play catch up.

As we begin to unpack options for an accounting (or financial) system, it’s important for me to explain the lenses from which I’m speaking.

First, I love the K.I.S.S. method. It means Keep It Simple (Stupid). Obviously it’s up to your discretion whether you use that last part of the acronym, but you get the point. If a system or process is too complex, it may not be worth your time right now. An overly complex system also makes it harder for the people around you to adopt or understand.

Second, think about price. If you’re starting from scratch, maybe consider a free or relatively cheap solution. Yes, you might want to grow into this massive system, but that’s the point – grow into it and not start with it.

And with that said, let’s jump into some options.

Wave Accounting

1. Wave

As a small business owner myself, Wave was my first go-to choice for when I started my business. I needed help getting started with my business financials because come tax time, I knew the IRS would be asking for financial statements, and I didn’t want to be working on it last minute.

It’s actually really easy to setup and use. I would get excited when the Wave notification came through on my phone too because an invoice had been paid by a customer.


  • Cost: $0 (Yes, it’s true!)
  • Included features: Accept Payments (standard credit card/ACH fees apply), Invoices, Bills, Bank Integration, Categorization of Expenses, Financial Statements, Other Reports
  • Additional features (at a cost): Payroll and Payroll Tax Filing


  • Customization: remember the K.I.S.S. method from above. Fewer customizations could be a negative but could also be a positive.
  • Target markets: great for small businesses and non-profits but not for a church. It does not have the concept of donations for a church so would not use it as a “front end” to your church attenders.


2. QuickBooks

Everyone knows that QuickBooks is a tried and true accounting system for small to medium-sized businesses. And you will often get complimentary offers from Intuit or QuickBooks partners for things like filing taxes through TurboTax, etc. It’s become a standard in the industry in that it integrates with almost everything, including most financial institutions.

Like Wave, QuickBooks is easy to setup and very user friendly. They continue to expand their offerings and improve on the “usability” of their software, which is why it’s one of the potential options.


  • Cost: Starting at $15/month
  • Available features: Accept Payments (standard credit card/ACH fees apply), Invoices, Bills, Bank Integration, Categorization of Expenses, Financial Statements, Payroll, Payroll Tax Payments, Other Reports


  • Price + Features: QuickBooks has a large “library” of additional options and features available, and each one of those come at an additional cost. Can you pay bills through QuickBooks? Yes, but at a higher cost per month. Can you run payroll? Yes, but at an additional cost per month for the plan + an additional cost per employee, per month. Their increased number of features compared to other options is great, but like I said, it comes at an added expense to your monthly subscription.
  • Automatic Tax Payments: This “con” actually bit an organization in the rear at one point. When you utilize QuickBooks’ payroll feature, it will calculate your quarterly tax payments necessary, but it will not pay those for you. You need to pay those manually.

When I look at possible software solutions, I look at it from a holistic lens and want to make sure all areas of a business are covered. This is why the automatic tax payments is an important “con” to consider if using QuickBooks for payroll because it can really hurt an organization if not handled correctly. For this reason and others, I recommend looking at Gusto as a payroll option versus QuickBooks.


3. Xero

Xero is my favorite option for any small to medium-sized business or organization, including churches. It incorporates all of the needs of financial reporting with bills, reconciliation and expense reporting. If your organization uses Gusto for payroll or Square for POS, it also has automatic integration options for those as well.

When you first launch into Xero, it could be a little daunting just like any other robust accounting and financial solution. However, once you get started, it runs very smoothly.


  • Cost: $12 or $34/month
  • Included features: Full accounting system with general ledger, Tracking categories to create departments and profit centers, Accept payments (standard credit card/ACH fees apply), Invoices, Bills, Bank Integration, Categorization of Expenses, Financial Statements, Other Reports
  • Additional integrations (some at a cost): Gusto, Square (through, Zapier, and many others


  • Robustness: With Xero being a robust system, it can be daunting to setup at first. However, Xero has a strong support team and user community to answer any questions that arise.
  • User Interface: The user interface itself has a difficult challenge of including everything you need while making it user friendly. This is always a delicate balance and continues to get better and better with time.
  • Reporting: The reporting features and capabilities continue to increase in usability and customization. If it doesn’t mean your organization’s needs, additional reporting vendors can be used instead (at a price).


These three options are my favorite and offer the most robustness, versatility and value across everything I’ve seen or been a part of in the past. Of course, there are some incredibly deeper and more robust options not mentioned. If you have the staff and financial resources for one of these solutions, go for it! I’m just trying to provide non-profits and small to medium-sized businesses with more value for your dollar. Have a question? Send a message.

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