3 Common Nonprofit Bookkeeping Challenges – and How to Solve Them

By Mike Depew
Published October 15, 2025 Oct 15, 2025

Many nonprofits struggle with bookkeeping tools that weren’t built for them. In our recent webinar with nonprofit accounting expert Jenn Viridis of Ethical Profits, we explored the top three accounting challenges facing nonprofits—and how MonkeyPod helps solve them.

Read on for a summary of the key takeaways from Jenn’s presentation. You can check out the full presentation by filling out the form at the bottom of this page.

1. Tracking Restricted Grants

Many nonprofits use systems like QuickBooks or Xero, which weren’t designed for nonprofit fund accounting–they are designed for for-profit businesses. That often means complicated workarounds, manual spreadsheets, and a high risk of human error.

MonkeyPod makes it easier:

  • Restricted and unrestricted funds are automatically tracked as dedicated net asset accounts on your chart of accounts.
  • Because you can use restricted net asset accounts to track grant funding, you can use classes to track what they are meant to track–functional categories. And as a bonus, the Statement of Functional Expenses you are required to submit to report on your functional categories is a built-in report in MonkeyPod.
  • You can simplify fund releases by releasing funds in the same step that you are recording the expense. And you still have the flexibility to do a separate fund release transaction if needed. No more confusing journal entries or mismatched reporting periods.
  • This keeps your funders happy by showing exactly how restricted dollars were spent.

“I’ve seen organizations lose grant renewals because they couldn’t produce the right reports,” Jenn explained. “They couldn't prove that they spent the money, that the way that the grantor wanted them to spend the funds. And as a result, they weren't able to get that funding the next time it rolled around.”

“MonkeyPod allows you to generate those reports with far less manual effort.”

2. Managing Reimbursable Grants (a.k.a. Contracts)

Reimbursable grants can be another headache in for-profit accounting systems—especially when QuickBooks charges extra for the features needed to manage them properly.

MonkeyPod simplifies the process with the Contract Tracker:

  • Tag reimbursable expenses to specific contracts with a simple dropdown.
  • Automatically track how much has been spent and how much is available to invoice.
  • Create invoices and track payments—all in one place.
  • Reduce errors and save money compared to QuickBooks Advanced plans.

“In QuickBooks, reimbursable grant features can cost over $3,000 a year,” Jenn noted. “It's going to cost you more than MonkeyPod just to do reimbursable grants, and that’s just one out of a dozen other things that you're going to need your accounting system to do for you.”

3. Keeping Teams in Sync

Many nonprofits struggle to keep their board members, bookkeepers, and executive directors on the same page. And as your organization grows and you have more staff, that only gets more complicated. Data is scattered across spreadsheets, CRMs, and accounting tools.

MonkeyPod brings everyone together:

  • Combines your CRM and accounting into a single, connected system.
  • Lets every team member access custom dashboards with the metrics that matter to them.
  • Tracks financial data and relationship info side by side—so you always see the full picture of your donors, funders, and partners.
  • Offers granular user permissions and unlimited users, so everyone gets the information they need without introducing additional risk.

“It keeps everyone in sync,” said Matt Radick of MonkeyPod. “You don’t have to worry about whether the executive director, board, or accountant have the same information because it’s all one data set.”

Bonus: Real-Time Budgets and Reports

MonkeyPod also makes budgeting easier with real-time updates, program-level rollups, and shared expense allocation. As soon as a transaction is entered, your reports update—so your team always knows where things stand.

Learn More

Want to see the full presentation from Jenn? Fill out the form below to get instant access for free.


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