While QuickBooks has been around for many years and is probably still the most used accounting software, there are many hidden costs when using an accounting software that is the least productive software.
Below is a link to download a Whitepaper on where most of this information is coming from. A CPA firm in California was the basis of this research and is currently used to show how Sage Intacct can help not only in accounting but in an overall processes where times is saved and resources minimized.
Now, the research presented four "factors [that] consistently slow down the monthly accounting process:
"Over-reliance on manual, paper-based processes
"Lack of integration between financials and other business critical applications
"Decreased staff productivity as a result of inefficient and lack of automated processes
"Inadequate data and lack of insight into the business" (Page 5)
To be fair, this statement was not for users specifically using QuickBooks, but the study does go on and say "This study corresponds with the main bottlenecks that QuickBooks users identify..." (Page 5)
In my experience, many small businesses and nonprofit organizations really align with the 4th bullet point in that they do lack proficient analytical data. And if they do have good analytical data, it is most likely through a manual process, using Excel. This presents a problem where the presented data is now separated from the original data source. When there is a disconnect between softwares, that dramatically increases the possibilities of errors.
Another time and error factor that nonprofits need to worry about is the ability to produce reports within the framework of fund accounting. This is where there is a large deficiency within QuickBooks. So many nonprofits extend their filing of their 990 because of the dependency on downloading their financial data into Excel and determining their nonprofit financials needed for their 990.
If you would like to read more, here is a link to download a report on the hidden costs within QuickBooks.