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Issues/Shortcomings of QuickBooks Online for larger companies

QuickBooks Online is a great accounting app.  As a matter of fact it is best in class in the market, you can purchase QBO for $35 to $200 a month based on the version you need.  However, it is still very far away from having feature/benefit parity to its Desktop/Enterprise counterpart; and for larger companies, it might not pass muster.  Here is my master list from an internal wishlist I have been compiling for years, it might serve a good context for you to know prior to moving from QuickBooks Desktop (or another more powerful accounting package such as Sage Intacct, Netsuite, MS Dynamics, etc) to QuickBooks Online.  I primary work with “larger” companies that are crossing that micro/small business segment and moving into the midsized segment; usually with 10+ employees and over $1,000,000 in case; and as the business gets more complex, the accounting software’s shortcomings start to really affect the operations and ability to grow.

I work with many QuickBooks Desktop Enterprise users and starting to get proactive requests from them to want to move to QuickBooks Online Advanced.  This is usually a complex conversation that requires a deep analysis of the operations to determine suitability.  The move from Enterprise to Online brings upon more feature loses than gains; and requires a close look.  If you are looking for a QB Desktop/Enterprise vs. QB Online/Advanced feature parity comparison guide, look at this spreadsheet

I also want to disclose that I am being idealistic here.. no software program is perfect and if I were to dig into QuickBooks Online’s competition such as Xero, Freshbooks, Zoho Books, Wave, Sage Accounting, Patriot, etc.  I will probably find a much biggest list of deficiencies; honestly all QuickBooks competitors are just straight garbage software which is why I have never bothered to look at something else… HOWEVER, I have been using QuickBooks for 20+ years and I hold them to a higher standard.  QuickBooks has become an extra limp for me over the years and I couldn’t do what I do without it, period.

Alright, here is my “wishlist” for QuickBooks Online as of 05/23/2022..


All Versions – Core Reports:

  • Sort by Amount on reports, for some crazy reason, you cannot do this; feels like a huge glitch 
  • Clean Excel report exports: right now the excel reports have all sorts or merging and formatting issues… could be useful to have clean/flat excel exports that are unformatted
  • Default Report setting: ability to set up any standard report to have a predetermined set of attributes: fields/columns, collapsed status, comparative columns, default debit/credit Columns for detail reports.
  • Management Reports revamp, ability to create truly customizable report packs that contain every type of report that Quickbooks can generate
  • Collapsed/Expanded Status saved in saved custom reports
  • Report Preference to set up a parent account to default as expanded or collapsed based on the setting.  So we can pick some parent account (with sub-accounts) to start collapsed or expanded by default – this would be a setting in the account itself inside the chart of accounts
  • Report Setting to turn on and off account numbers on the fly (no need to go into reference) for a specific report
  • Report Setting to make all account names temporary UPPER CASE or PROPER CASE (in other words, override the current state)
  • Full path mode for summary reports (so the accounts do not show in a hierarchy, rather they show their full path like in the trial balance report, such as: Car & Truck: Gas
  • Trial Balance by Class or Trial Balance by Location… or the ability to filter the trial balance by either one of this
  • Tags in the group by or columns by for other reports.. not just limited to the tags report
  • A simple Custom Transaction Detail report, like the one in desktop.  Also make sure that a report like that can also report on non-posting transactions like estimates, purchase orders, delayed charges, time entries, etc.  This type of report would be perfect to use to create a report deriving from a FIND/Search query
  • A simple Custom Summary Report like the one in desktop.  And/or add more fields to the current summary report
  • Customer Type available in reports as the group by or columns by
  • Inventory Valuation Report by Location or ability to use the locations filter in this report!  This is without having to create multiple inventory site features inside the software as a feature, sometimes this could help as a workaround.
  • Sales by State, Zip Code, and by City (particularly important to reconcile sales tax) – this should be both for bill to and ship to locations
  • Simple to read Undeposited Funds report that can show items waiting to be deposited and/or deposited items to payments linked in the report
  • Add the many missing fields from reports, such as Payment Method
  • Ability to customize a report to add Gross Profit Margin under the Gross Profit amount.  And Operating Margin under Operating Income amount.  I don’t want all the %ages on the right of the amounts, I just want Gross Profit Margin and Operating Margin below the $ amount, not to the right of it as a separate column.
  • Ability to sort on the A/P Aging Detail Report. Of course, they would still be grouped under “current”, and “1-30 days past due”. But within those groups, I’d like to be able to sort by vendor, or by amount, or by number.
  • In Estimates & Progress Invoicing Summary by Customer Report, be able to exclude completed estimates so that it doesn’t always show every estimate ever written
  • Ability to choose Items in bank feeds instead of accounts (as an option)


All Versions – Other Areas:

  • Ability to make company file duplicates, this is integral to doing tests with new apps
  • Chronobooks (ability to backup and restore), IMO, it should be available in all versions and they must integrate it into QBO is it does NOT feel like a 3rd party app
  • QBTime, needs to be redesigned to look and feel the same as QBO (like an internal addon, not a 3rd party app.  I am OK with this costing extra
  • OneSaas, same as above
  • QBCommerce, same as above, and honestly, it should be an Addon exclusive to Advance, maybe a sku called “QuickBooks Advanced with Commerce”
  • Make QBSE upgradable to QB Simple Start or Essentials
  • Merge Simple Start and Essentials skus… make essentials maybe $30/m but do not have a SS option at all, you can make QBSE $15/m but allow users to move to essentials (migration) whenever they need to.
  • Ability to restrict a user from using Transfers or Credit Card Payments in banking.  The Uncategorized Asset categorization is a real issue
  • Consistent UI with date pickers, checkboxes, shift click, keyboard shortcuts across entire experience
  • Ability to completely turn off the suggestions in bank feeds – and also turn OFF the auto-add rule option all together
  • Speed up the process in which you get banks added to bank feeds and participate in bank statement fetching
  • Stop ALL advertising of new services within product (QB Live, Merchant, Payroll, QBcommerce, QBTime, new apps, etc..) when an accountant is attached to the file
  • Ability to permanently delete customers, vendors, items, accounts that have ZERO transactions associated with it.
  • Mark all transactions “CLEARED” on the transaction screen when looking at them when they have cleared the bank 
  • Sorting, filtering, and grouping inside Undeposited Funds screen when creating deposits. 
  • Make sure checks written to customers (such as for a refund) show up in the transaction list by customer
  • Invoice or Sales receipt to Credit memo (or refund) workflow
  • Show project, memo, class, location, and/or expense category in bill pay screen – Option to transfer memo field from bills onto bill payment memos
  • Add classes, locations, and tags to several screens missing them – Also the ability to turn OFF tags the same way classes/locations can be turned off
  • Ability to use multiple A/R and multiple A/P accounts like in desktop
  • Upload PDF bank statements to bank feeds when direct connection or CSV is unavailable (using MoneyThumb’s technology)
  • Fix the “Sticky” left navigation bar issue, where the submenu gets stuck even when there is no mouse cursor on top of it
  • When adding or changing Customer and/or Vendor address inside a transaction or email fields in a form, prompt to save back to Customer or Vendor record.
  • Add support for vendor discounts when paying Bills early
  • Price rules: complete this tool, it has been on “beta” since 2019
  • Dynamic font and space resizing when making browser windows other than full screen, particularly important for laptop users without 2 screens.
  • Include Add subtotal line option on Sales Receipts so it matches invoices
  • In Progress Invoicing, be able to invoice by partial quantity, not just % or $
  • Need more detail in 1099 toggle – not just on or off, but why, (SMLLC, CORP, PS, etc.), so we don’t have to look for notes every year.
  • Need ability to add Customer/Project Column to Open Invoices and Unpaid Bills/Aging Reports.


QBO Advanced – Inventory FeaturesAssuming QB Advanced will not have a QBA+Commerce style of integration, then it needs to have several inventory-related enhancements:

  • Sales Orders: the ability to have a sales order that backorders a sale to be converted to an Invoice later on
  • Customer Prepayments: ability to take in payments from customers without a sales receipt or invoice present.  Ideally this payment will be attached to the Sales Order somehow
  • Multiple warehouse locations, no need for Bin numbers immediately, but Sub:locations could be used for that purpose
  • Lead time: ability to have a filed in the item for lead time (in days)
  • Multiple Preferred Vendors: ability to have a different  cost, purchase description, and lead time based on multiple preferred versions 
  • Vendor Prepayments: ability to make a payment to a vendor related to inventory but link it to the PO prior to it being received
  • Landed Cost: the ability to take costs from bills, checks, expenses, and/or credit card charges into inventory item’s value
  • Lot Numbers: ability to track inventory by lot number, and the accompanying lot number reports
  • Invoice profitability preview: ability to preview the profit and gross margin inside of a sales order or invoice
  • Inventory stock status by item report: know what you have in stock, what is on backorder (sales orders), and what is on Purchase order
  • Item attributes: ability to give items specific attributes to be able to report and filter by that attribute, these could be item level custom fields
  • Reports by Item Category, by Preferred Vendor, by Item Attributes, by Income Account, by COGS account, or by Inventory Asset Account
  • List price: in addition to sales price, being able to see the list price AND the sales price in the form so customers can see the discounts.  Also Price Rules could interact with list price as well
  • Multiple Ship to addresses per customer
  • Ability to add line-item level discounts (amount and/or percentage) that is visible as a column so customers can see the “retail price” vs discounted price 
  • Barcode support: Support USB barcodes and using the mobile app
  • Serial number support: can also be scanned in using a barcode
  • Expiration dates: assignable to an lot number
  • Multiple Ship to locations for customers
  • Pick/Pack/ship fulfillment workflow
  • Multiple Units of Measure: we need to able to have multiple units of measure for inventory management
  • Volume pricing and MuM pricing: individual prices to the “bundled” items using MuM and/or sales price based on volume
  • Inventory Assembly: for manufacturers this is essential
  • Inventory Aging Report: to know which inventory item is at risk of obsolescence
  • Inventory value Adjustment
  • Disallow Negative Inventory sales and Negative Inventory Reports
  • Fifo Lot valuation reports: ability to know how many of the inventory on hand is available and at what FIFO cost
  • Min/Max Reorder points and automatic PO workflow by preferred vendor
  • Inventory Forecasting: based on historical sales, current inventory levels, AND Sales orders on BO
  • Use item picture in the sales transaction or as an attachment


QBO Payroll and Sales Tax

  • More flexibility and control when editing and adjusting payroll – specially the ability to edit paychecks for periods in which the forms have not yet been filed; this could be opened up for accountants or advanced users only, possibly… but we need access to editing things without needing to contact support
  • Certified Payroll in QBO Payroll
  • Support for Ag employers (Form 943 filers)
  • Comprehensive and up to date payroll education for both end users and accountants – to contain detailed step by step setup/configuration process, understanding on how the mechanics of payroll work, education on the actual payroll forms, and how to troubleshoot issues – to reduce the burden on tech support for payroll, which feels significant
  • Multiple source bank account support for payroll. Such as the ability to pay paychecks and taxes from different accounts; or paying different groups of employees from different accounts (useful for businesses with multiple locations)
  • Ability to use full tags, classes, locations, custom fields in payroll at the payroll item level as well
  • Payroll summary report (same as Desktop) with full filtering and grouping flexibility 
  • Payroll job costing by Project in GL: we need the cost data of the paychecks in our regular P&L reports, it can’t just live inside Projects
  • Multiple pay type that are mapped to different accounts
  • Allow payroll items to point to NON-liability accounts – when I reimburse an employee for fuel, I want that to offset fuel expense, not sit in a PR liability account until I remember to move it.
  • Fixing the Sales Tax center, it’s a disaster (might need another separate document to detail all the issues with it) – for the time being, fully customizable/filterable sales tax reports that allow the user to manually check if the numbers (taxable vs. non-taxable) are being reported correctly to prepare the tax return manually with good information.


QBO Advanced – Specific to Project-based business:

  • Convert a timesheet by Vendor to Bill: QB desktop does this, this is crucial!
  • Projects in reports: we need to be able to run reports by Project and not just by customer.
  • Project status: we need to be able to know the status of a project (started, WIP, completed) and the estimated completion date.  Make project status available in all reports that contain a Customer filter. 
  • Project Type dropdown that allows to group or filter projects by a specific type.  Similar to how customer type would work.  Another solution would also be to add customer type as an attribute to project type
  • Dates for Projects: start date, estimated completion date, actual completion date, etc…
  • Default Location or Tag by Project: ability to automatically assign a location or tag when the project is selected, at least on sales transactions 
  • Customer Type: needs to be available in reports, grouping by Customer Type or filtering 
  • Multiple classes inside Payroll, taking the class data from the timesheets and bring that into payroll
  • Projects available in the API across the board.
  • Cost and Markup inside estimates to be able to produce Estimates vs. Actual Reports
  • Cost to Complete and WIP Summary Reports with Percent of Completion
  • Workers Comp cost allocation by project
  • Include vendor name into estimates for internal projected cost management.  This would allow for a Estimate to Bill or Estimate to Purchase Order workflow that would retain the vendor info including projected/negotiated cost that is entered into the stimate
  • Change Order Tracking: special estimates with a Change order attribute that can be used to report separately
  • Customizable Commission reports: ability to choose if the sales rep is being represented in a custom field, tag, location, or class.  In other words a percentage gets multiplied by Total Income, Gross Income, or Net Income based on any of those four dimensions 
  • Billing Rates by employee. When an invoice is created from allocated time in a timesheet, the rate of the employee should vary based on that billing rate
  • Mark all billable or Mark none billable button for bills/expenses with customer:projects assigned
  • Change/edit address or ship to location at the project level
  • Handle WIP projects correctly in accrual AND cash basis. In desktop, we have the ability to create pending invoices that help with customer deposits and partial customer payments


QBO Advanced –  Other General functions:

  • Fully customizable reports with pivot table style reporting, and ALL fields need to be available. (IN PROGRESS WITH CUSTOM REPORT BUILDER BETA)
  • User permissions: high level of detail and customizability to the multi user structure – also Phone app custom permission: choose what does the phone app user have access to
  • Customer level or vendor level user permissions (so the user can only access certain customer and/or vendors)
  • Built-in multiple file report consolidation, without using Fathom
  • Customer credit limits, with warnings and permission level restrictions
  • Ability to restrict user from selling at a different price as sales price, or a specific amount/percentage above/below cost or list price
  • Access all the additional Accountant-only features such as: Month-end review, Write Off, Undo Reconciliations, etc.


API / Data management / MISC

  • If Sales Orders and other features are added, the API must have access to sales orders, multiple warehouses, U/M, etc.
  • OnceSaas needs to take transactions from the multiple channels and bring them into QBO as Sales Orders
  • Custom Fields need to be in the API
  • Tags need to be in the API
  • Projects need to be in the API
  • Banking needs to be accessible via API
  • Easy to read reference sheet for NON DEVELOPERS with list of transactions and fields available in the API
  • Fully functional PowerBI integration
  • Ability to backup an “offline” read-only version of the data into a QBO desktop app to be able to access the archive of data for 3-7 years after the company closes to comply with auditing regulations.  Alternatively, keep the data alive (online) for 7 years after the company closes.
  • Ability to simply DUPLICATE QBO company files, that immediately open a second subscription with a 30-day trial, this is useful for people that are going to add an app and worried about the repercussions of the data sync; which is what holds people back for adding apps.  Also, its valuable to duplicate the file to create a testing/training environment without fear of what would happen to the “live” file
  • Set the “already seen” flags for in-product pop-up suggestions as part of the user’s server-side permanent settings rather than in cookies
  • When converting from QB Desktop to QBO, we need the attachments to come in with the conversion to QBO.
  • QBO to Desktop conversion/backup needs to work 100% of the time, businesses close all the time, we need to have a permanent backup for audit purposes (for 7 years, Intuit is not going to keep that account live for that long…)
  • SpreadsheetSync (Beta) needs to be completed to bring ALL data fields, otherwise is not useful (this is an API issue)


Special Advanced and/or Accountant Tools:

  • Reclassify tool should be able to change: source account, vendor/payee, customer:job.  Also add Shift-click experience to the tool so be able to easily select a group of transactions to batch
  • Batch enter (copy/paste) experience needs to be fixed, it hardly ever works, fields do not get recognized correctly, it doesn’t really save anyone any time
  • Ability to correct or add missing vendor/payees in batch 
  • Import ALL transaction types via CSV. Apps like Transaction Pro and SaasAnt should not exist, QBO should have all those capabilities built-in, especially Journal entries!
  • Easy CSV import for timesheet data
  • Batch Edit: ability to edit several transactions in batch for any transaction type
  • Accountants should have access to ALL tools and all reports when accessing client files, regardless of their subscription level
  • Customer Service prioritization to power users and accountants – Intuit top/knowledgeable team should be available to advanced and accountant users with a 15 mins max wait via phone call or chat.  Cross train the Bookkeeping live people to serve as overflow – I am comfortable with paying an annual fee to be a ProAdvisor to have this level of service… The free ProAdvisor issue gives Intuit TOO MANY users to serve, and your best users do not get the priority they deserve.
  • Ability to disable Bank Feeds for non-accountants when an accountant is connected to the file
  • Fixed Asset and depreciation management
  • True “Accountant Mode” vs. “Business View” where the accountant gets all the tools and technical terminology vs the simplified version for a business owner.  Accountant’s Mode gets zero popups and warnings
  • Chart of accounts locking: ability to block a user from creating, deleting, or merging accounts in the COA. At the same time, ability to block a user from using a PARENT account when subaccounts are present
  • Cost allocation tool: at allows to take overhead expenses that do not have a class (item level) or projects assigned to them, and adjustment them against all the active (or selected) classes and/or projects; so the P&L by class and P&L by Project does not have an unclassified column
  • Ability to “Undelete” or restore deleted transactions like a recycle bin(trash)
  • Chart of Accounts “batch cleanup” tool that allows for easy renaming, renumbering, merging, reclassify type, make sub-account or make parent account, of the chart of accountants in batch.  Including ability to import your own chart of accounts and quickly remap a currently account with transactions/history into the newly imported one


Specifically for Accountants supporting multiple clients:

  • A write-up only version for QuickBooks Online, that is $10/m or something affordable to be able to bring all of our non-QB facing customers into QBO (and presumably out of QB Desktop or spreadsheets).  This version of QuickBooks Online would be limited to Banking, Journal Entries, and Reports.  This is for our quarterly and annual write up clients that will not be accessing QuickBooks, or invoicing, etc.  – Maybe this could be sold in packages of 5 for $50 a month, or something like that…
  • Additionally a low cost ($10 as well) add-on for after the fact payroll support, so accountants can have a tool to produce quarterly payroll for their small clients.
  • A custom set or group of reports, chart of accounts, bank rules, preferences, etc. that you can copy across all clients.


-Hector Garcia, CPA & Advanced QuickBooks ProAdvisor

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Hector Garcia

Hector Garcia

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