Comparing The Best Accounts Payable Software For Startups

Bethany Mullinix
5 min read
Comparing The Best Accounts Payable Software For Startups

Automating tedious day-to-day tasks, like your accounts payable (AP) processes, is an efficient way to take the pressure off your shoulders when running a startup. 

But you know this. Your startup is probably also using AI to make someone else’s life easier. So why not yours? 

AP is one of the most important areas of your business that you can automate. Disorganized and inefficient AP processes can lead to late fees for missed payments, inconsistent cash flow projections, and strained vendor relationships. To free up time and enhance efficiency, let software do the brunt of the work. 

In this article, we will look at the best account payable software for startups on the market. We’ll explore the features and benefits of each and give you a side-by-side comparison of how each measures up so you can decide how to automate your AP. 

Skip right to the good stuff and get a personalized 1-1 consultation here to see which AP software is right for your startup.

Why Should Startups Use AP Software?

As we mentioned, automating your bill pay processes can transform your accounts payable operations. It’s a no-brainer in our eyes, but in case you need a little more convincing, we think these 4 reasons are pretty killer:

1. It saves you time – You weren’t born just to pay bills and die. If it feels this way, you're doing it wrong. Automation gives you your life back AND lets you get back to running your business.

2. It eliminates the chance of error – Instead of manually inputting your vendor information and invoice details each time, AI software can auto-fill all the information in seconds and remember it for future payments and classifications.

3. It increases efficiency – Stop chasing down vendors and managers for approvals. Automation removes manual approval flows or data entry, reducing the time and effort required to process and pay bills.

4. It saves you money – Ultimately, automating AP saves money because of the three previous benefits we discussed. You pay less for salaries and hourly rates than you would to manage the process manually. And with the right software, you may save money on subscriptions and fees. More on that below!

How To Choose The Best AP Software For Your Startup

There are a lot of different options out there when it comes to financial software. So how do you choose the best software for accounts payable? Here are a few things to keep in mind:

  • Ease of use: The software should be easy to use and navigate, especially if you’re not planning on hiring a bookkeeper for a while. If you are the one using it, you’ll need to understand how to set it up, run it, and contact support. 
  • Features: Ensure the software has all the features you need for your business. Do you need all-in-one accounting or just the basic features? Do you want to bundle accounts payable and accounts receivable? 
  • Pricing: You don’t want to skimp on good software, but you must be realistic about what your company can afford. Pay attention to processing fees, how many users you’ll have, and if there’s a percentage fee for credit/debit use. 
  • Invoice Amount: If you don’t process that many invoices monthly, you don’t need the most robust invoice processing software. If you have more than 10 bills per month, you might need a dedicated team to help you handle the workload.

Keep these factors in mind as you read through our in-depth analysis of four different types of accounts payable software. 

Below we’ll compare Zeni,, Melio, and Plooto. 

Pros and Cons of the Best AP Software

Zeni Bill Pay

Zeni Bill Pay Dashboard

Zeni Bill Pay is the fastest way to pay vendors and automate your accounts payable process from start to finish directly from the Zeni Dashboard. And it’s 100 free! Whether you’re new to Zeni or an existing customer, it’s the easiest, most cost-effective way to pay vendors and contractors with minimal management of the process on your end. 

If you need extra support, Zeni offers additional AP management services. Its team of startup-focused controllers handles all administrative tasks related to maintaining an up-to-date AP process, like vendor management, email communication, and of course, making your bills get paid on time. It’s free to add on if you’re processing less than 10 bills per month.  


  • It’s free! – Use Bill Pay at no additional cost to your existing Zeni subscription and $0 ACH fees.
  • Eliminate chances of error – Simply upload an invoice, and AI auto-fills all the information in seconds.
  • Save time – No manual entry and automated approval flows make payment to vendors hassle-free.
  • One powerful dashboard – The dashboard you already use as a Zeni customer tracks payments and statuses (plus all your other financials) in one place.
  • Real-time updates – Zeni AI processes your invoices in real-time and updates your books daily instead of at month-end. With real-time reporting and analytics, you can have greater visibility into the status of your bills, payment history, and overall financial health. 
  • View payment summaries and trends See monthly and yearly bill payment trends to better understand where your money is going.
  • Customize the approval process – Customize internal approval rules based on bill amounts.
  • Better integrations – Less syncing error with the finance tools you already use, like Quickbooks Online.
  • Most affordable AP management – Anyone can use Bill Pay for free, but Zeni is one of the few AP platforms to offer complete management of the entire AP process by a dedicated controller. The service costs extra after ten bills per month. 


  • No international payments or credit cards – Zeni plans to roll out international and credit card payments in early 2023. Any company already using Zeni Bill Pay at the time of its international launch will have priority access and receive competitive pricing. 
  • No accounts receivable Zeni is still building its AR capabilities but is exploring adding this function soon. In the meantime, Zeni Bill Pay allows companies to save instantly on their AP services. 

Learn more about Zeni Bill Pay here

BILL homepage

BILL has been a widely known automated accounts payable solution serving the business world since 2006. It focuses on giving businesses a centralized way to manage accounts payable, accounts receivable, and expenses. Since it is a little more robust than most AP solutions, it’s best suited for mid-sized businesses rather than smaller startups.


  • Extensive integrations – BILL connects with many leading accounting tools, helping reduce manual entry, speed up account reconciliation, and simplify your workflow.
  • Multiple payment options – Process payments faster with options including ACH, check, international wire, and credit card payments. 
  • Mobile app – BILL has a dedicated mobile app to manage your entire AP process from anywhere, including setting payment reminders and notifications and uploading invoices. 
  • Manage AR – Easily set up clean invoices that you can track directly through the BILL platform and receive payment back to your bank account.  


  • Limitations around integrations – Unless you use Quickbooks or Xero, you’ll have to upgrade to an additional tier for software integration. Smaller tiers like the “Essentials” plan also do not include integrations at all and require manual import into accounting software.  
  • Extensive platform fees - Per user charge for all plans and even more for custom enterprise plans (average $3,300 per year) and payment processing.
  • High transaction fees – BILL has some of the highest transaction fees compared to other accounts payable software tools on the market. 
  • No real-time accounting sync – While BILL connects to most accounting tools and you can track your payment statuses in real-time, you won’t have access to real-time numbers and account reconciliation.


Melio homepage

Melio Payments is an online payment platform that allows businesses to send and receive payments globally. The platform gives users a more flexible way to pay and keep track of business bills (both AR and AP) in one simple-to-use dashboard. Accountants and bookkeepers can also use Melio to manage their clients’ info in one place.


  • Payment option flexibility – Besides ACH and paper check payments, Melio lets you pay a bill by credit card even if the vendor doesn’t accept them and vice versa. This flexibility potentially helps you maximize and extend your cash flow.
  • International payment support Supports payments in various currencies which can reduce the high fees associated with currency conversion. They also offer a competitive exchange rate.
  • Batch bill payments and partial payments – Pay multiple bills simultaneously or make partial payments. 
  • Earn rewards – Melio encourages you to pay by card to earn rewards and cash back when you pay your bills on time.
  • Accounting software sync Set up Melio to sync to Quickbooks, Freshbooks, Xero, or Microsoft Dynamics 365 Business Central, so you aren’t entering data in 2 places.
  • Free platform use – You can use Melio for free but might incur the fees mentioned below in the next section.


  • High transaction fees – This applies to credit or debit card transactions, international payments, and expedited bank transfers (same-day ACH payments). 
  • No accounting or bookkeeping capabilities – While Melio syncs to your existing bookkeeping software, you can’t perform any bookkeeping or accounting functions outside of AR and AP with Melio. So you’re still going to multiple places to access your financial data. 


Plooto homepage

Plooto is a cloud-based payments platform that automates AP and AR processes for startups and small businesses. Its goal is to help you better manage your business’s cash, eliminate paperwork, maximize efficiency, and find early-payment discounts. 

Plooto is based out of Toronto, Ontario, and calls special attention to its CRA remittance capabilities, offering a place for Canadian businesses to make remittance payments through the same platform as their other AP and AR operations. 


  • Both AP and AR capabilities – Whether money is going in or out, you can easily manage both sides of the bill pay process through Plooto.
  • International payments – Transfer money across 40+ countries for a flat fee and check exchange rates directly within the platform. 
  • Multiple payment options – Make batch or single payments by paper check, bank transfer, or credit card.
  • CRA Remittance – Canadian customers can pay remittances like payroll and tax payments in one place.
  • Recurring payments – Set up an automatic payment cadence for bills, subscriptions, and other expenses that you have monthly.
  • Seamless integrations – Link Plooto directly to your Quickbooks or Xero accounting software for automatic reconciliations and to reduce data entry.
  • Approval workflow creation – Customizable approval tiers and workflows for unlimited vendors and approvers under one price. 
  • Free trial – If you’re on the fence, you can try Plooto for free for 30 days.


  • No freebies – You’ll need to pay for the platform and per-transaction fees
  • No same-day ACH – You can add funds to Plooto’s digital wallet to pay vendors faster, but there are no same-day options if you’re in a pinch.
  • No AP service team – While the automation Plooto has in place will help speed things along, you’ll still need to manage the system on your own or through an accountant

Head-To-Head Platform Comparison And Pricing

Let’s look at each of these AP platforms side-by-side. 

Combining Automated Bookkeeping And Best Accounts Payable Software

As you can seen, there are many options out there if you’re looking for accounts payable software with many different capabilities, but ultimately it comes down to which platform will create the most efficiency for your team, be the easiest to use, and save you money.

On top of that, be sure to consider which services will best streamline your entire financial operations. When you can connect a small part of your finances, like AP, to the bigger picture and every piece of financial data you have in a single place, you can increase decision velocity for your startup.

If you want to check out Zeni Bill Pay for free and Zeni’s holistic view of your finops, we’ve got you covered here.  

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