The 6 Best Apps for Retail Businesses

I know you came here searching for the six best apps for retail businesses. This is an area that goes both so wide and so deep, that to put a list like this together, and call it absolute would be next to impossible. So, I’m going to outline the top six apps for retail business that I’m currently researching for my business and clients.

To sum it all up: The ecommerce industry has failed the accounting industry. There are many applications that handle almost all of the process really well. The accounting part is where almost all of these applications fall short.

The issue with the “best apps for retail business” is that there are many moving parts in the process, so it depends on which parts of the process are most critical for you. It may be all of them.

Here are the steps in a retail flow, focusing on an online business, which is where this gets infinitely complex.

  • Selling points (where the sale is made: Amazon, eBay, your website, etc.)
  • Payment processing
  • Inventory management
  • Accounting integration
    1. Pushing the sale and related inventory components to the accounting software.
    2. Reconciling sales with payments funded in the bank account.

This is a very high-level outline of the process. Within the above, you may want CRM capabilities, purchasing, reorder quantity management, receiving, product management, assemblies, quote/estimates, multiple sales channels, email handling and management, and, of course, reports. That list is not exhaustive, so as you can see, this can be exhausting.

The ideal solution would let me manage my sales and inventory with multiple locations, across multiple sales channels, and automatically push the sales, inventory, and cost of goods sold back to my accounting software, all while reconciling the funds received so that it matches up perfectly with my banking.

Every single one of these applications handles all of this really well, right up to the very last piece. Not one of these applications handles this reconciliation piece well. Most don’t handle it at all.

That being said, with all the above considered, here are the top six apps for retail businesses in alphabetical order:

  • Agiliron
  • Dear Inventory

  • SalesPad Cloud

  • Shopify

  • Webgility

  • WooCommerce

You can view the mind map I made of these apps to see how they evolve over time. Feel free to bookmark it and check back for updates. Click on an app in the mind map, and you’ll find notes and links based on my research.

The 6 Best Apps for Retail Businesses


For multiple sales channels, Agiliron may be your first choice. The product was built for this, specifically, and it also has all of the other important components from inventory management (including the ability to track kits and assemblies), as well as CRM capabilities, and everything else listed above.

I have not been able to test payment processing on this (or any of the other applications yet). This is hard to do without a live use case.

The next thing that inspires confidence for me in Agiliron is in checking on the assemblies capabilities, I did a search in the help area for this and immediately found exactly what I was looking for.

The user interface is clear and clean. It isn’t difficult at all to see what is available and find what I am looking for. This is important.

Agiliron can get expensive though. That might be the one downside, but it if solves your multi-sales channel, inventory management issues, then it may well be worth it.

Dear Inventory

Dear Inventory might win on the user interface. That’s what initially got my attention. As I dug in and looked at the features that this solution offers, I realized that this application, when connected with QuickBooks Online, gives you all of the functionality of QuickBooks Enterprise Solutions with advanced inventory. And it actually costs less!

Dear Inventory lacks management of multiple sales channels, but you can integrate it with many online stores, such as Amazon, eBay, Shopify, Magento, and many others. The sales channels can all be managed and integrated within Dear Inventory, but you won’t be able to see them separately. This might or might not matter to you, so it really depends on your needs.

I read a few bad reviews about Dear Inventory, specifically about customer service, but so far, I reached out with a question and received an answer via email almost immediately. So far so good for me on customer service.

SalesPad Cloud

SalesPad cloud is a newer option that offers a lot of promise. They do not appear to have the ability to manage multiple sales channels, but it does have assemblies. The integrations on this one are also limited (for now). They integrate with QuickBooks Online, Shopify, Ship Station, and something called “PayFabric” which I’ve honestly not heard of.

From what I can tell so far, it looks like SalesPad Cloud is priced at a very straight-forward $99/user/month. If you don’t need multiple sales channels or a lot of integrations, this might be the best choice for you.


Every other one of these apps can integrate with Shopify, and Shopify lets you sell on Facebook. The bottom line on this one is that it isn’t even a question. At this point, I don’t care what business you are in. Your customers are on Facebook. Many of them practically live there. Set up your store in Shopify and then connect Shopify to whichever of these other apps you choose. It seems crazy not to use this app!


Webgility is one of the more popular apps for retail businesses. This is the one that most definitely lets you set up one central location to bring in sales from all of your sales channels.

Webgility also pushes all of your sales seamlessly back to QuickBooks Online. This might actually be the perfect solution, but we’ve run into one major snag. This is specific to selling on Amazon. Webgility will push all of your sales for a particular day to QuickBooks. The problem comes up if, for some reason, one of those orders doesn’t ship. In this case, while Webgility pushes all of the orders through, Amazon doesn’t fund them all. This gets us to the reconciliation nightmare, because now you have to figure out which sales funded and when the remaining ones will.

Webgility, by itself, does not manage your inventory. The best way to think of Webgility is a sales processing tool that will get the sales from your online store to your accounting software. This could solve 90% of your e-commerce problems but still doesn’t solve the reconciliation issue. And I wouldn’t count on using this with Amazon unless it is extremely rare that something in your online store doesn’t ship.


I couldn’t leave this one off the list because it’s the one I use for my own business. But before you run out and get it for that reason, read on. It’s not for everyone. If you sell products and have to manage your inventory, then any of the other solutions I’ve mentioned above, especially Agiliron, Dear Inventory, and SalesPad, will prove to be better options.

WooCommerce works for me, because all of my products are digital. WooCommerce does have inventory features, but updating this is very manual, in particular when it comes to adding purchases to your product quantities.

If you sell digital products, subscriptions, or memberships, then WooCommerce is great. It does not have an accounting integration built in, but it is very easy to export a CSV file of your orders and use Transaction Pro Importer to import your sales into QuickBooks Online.

WooCommerce is also great if your website is built in WordPress.

WooCommerce does have a plugin for Square, so if you have Square as the sole processing solution on all of your websites, then WooCommerce plus the Square integration could work for your product-based business.

Square also integrates with Dear Inventory—if you wind up going with Dear Inventory for inventory management, you could conceivably use WooCommerce and Square, and that might complete your ecosystem. I probably could have included Square itself on this list, but I would be here forever if I were to include all of the best apps for retail businesses!

The Bottom Line

There is no one size fits all solution, and in all likelihood, you need more than one solution to complete the entire picture. In the video above, I give an overview and a quick look at each of these applications. Then I show you how you can begin to map out your sales process so that you can start to fill in the pieces.

Whatever you have going on, there is one thing you absolutely must count on. Plan on spending some time doing your research. Implementing the wrong solution can be costly, both in terms of time and money. Your best bet is to hire someone who really knows this area well.

Seth David

Seth David is the chief nerd and president of Nerd Enterprises, Inc. which provides consulting and training services in accounting and productivity based software. Consulting services range from basic bookkeeping to CFO-level services such as financial modeling.

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