Best Invoicing Software for Virtual Assistants: Retainers and Hourly Billing

The right invoicing software for a virtual assistant is one that sends a monthly retainer invoice on its own, tracks the extra hours you work, turns those hours into an invoice line, and lets clients pay online. The five tools below all describe recurring invoices and online payments on their own pages. They differ in how they handle time tracking and retainers.

Billed publishes this page and is listed first. The other tools are listed alphabetically and aren't ranked. Every detail comes from each vendor's own pages, opened on October 29, 2026. Features and plans change, so check each vendor's site and pricing page before you sign up. This page doesn't list prices.

What virtual assistants need from invoicing software

• Recurring invoices for monthly retainers.
• Time tracking that turns logged hours into invoice lines, for work beyond the retainer.
• Online payments by card or bank transfer.
• Reminders for overdue invoices.
• Separate client records, so each client's invoices and payments stay together.

The tools

Billed

From Billed's own pages:

• Retainers: its recurring invoices page says: "Establish a stable cash flow with retainers. Negotiating fixed prices and sending recurring invoices makes it easier for you to forecast your income and upcoming workload."
• Time tracking: its time tracking page says you can "Log the time you and your team spend on tasks and projects, see it by day and by week, create timesheets, and invoice hourly projects from the time you tracked." It adds: "Create an hourly rate project, set its hourly rate, and Billed tracks the charge for each task as you log it."
• Payments and reminders: its invoice software page says: "Connect your Stripe account and every invoice you send gets a pay button, so clients can pay by card. Connect PayPal to add a PayPal option as well." It also says: "Payment reminders can be customized."
• Currencies: its features page says: "Invoice your customers in multiple currencies. Choose different currency for each invoice or customer."

Plans are on Billed's pricing page.

FreshBooks

From FreshBooks' invoicing page and time tracking page:

• Retainers: "Dedicate a specific number of hours to your client's retainer and schedule work against that amount at a pace that works for both you and your client."
• Time tracking: "Just start a timer and get down to business – when you're done, you'll have an accurate time log ready to pop onto an invoice."
• Billing and payments: "Automate your entire billing workflow, from recurring invoices and card-on-file payments to sending reminders and charging late fees."

QuickBooks

From QuickBooks' invoicing page:

• "Need to send out invoices on a regular basis? QuickBooks makes it easy to set them up automatically. Just use recurring invoices!"
• "Accept cards, ACH, Apple Pay®, PayPal, and Venmo, and manage it all right in QuickBooks."

Wave

From Wave's invoicing page:

• "Set up recurring invoices and automatic credit card payments for your repeat customers and stop chasing payments."
• With a Pay now button on the invoice, customers can "pay instantly by credit card or secure bank payment (ACH/EFT)".

Zoho Invoice

From Zoho Invoice's product page:

• Recurring invoices: "With Zoho Invoice, automatically generate and send invoices on schedule with zero manual effort."
• Time tracking: "Track billable hours, invoice timesheets, and charge customers accurately."
• Payments and reminders: "Collect payments via credit or debit cards, ACH, or e-wallets with online payment gateways." Zoho also says you can "Send payment reminders using Zoho Invoice".

Worked example (sample figures)

A sample virtual assistant, invented for this example, has a client on a monthly retainer of $900.00 for 20 hours. Hours beyond the retainer are billed at $45.00 an hour. In April the assistant logged 26.5 hours for this client.

• Hours beyond the retainer: 26.5 − 20 = 6.5 hours
• Extra hours charge: 6.5 × $45.00 = $292.50
• April invoice: $900.00 retainer + $292.50 = $1,192.50

Putting the retainer and the extra hours on separate lines, with the hours shown, lets the client see exactly what they're paying for. A recurring invoice can carry the $900.00 retainer each month; the extra hours change, so add them as a separate line from your time log.

How to choose

1. List how you charge: a fixed retainer, hourly, or both.
2. Check each must-have on the vendor's own pages: recurring invoices, time tracking, how clients can pay, and reminders.
3. Check the price on each vendor's pricing page, including payment processing fees and any per-user charges if you have a team.
4. Try it with a real month: log time for one client, create the invoice, and pay it yourself.

When this guide isn't for you

If you run a VA agency with a team of assistants and need payroll or contractor payments, check whether a platform's own pages describe those as well as invoicing.

Related Articles

• How to Build Freelance Retainer Clients
• How to Set Freelance Rates
• Recurring Invoices Guide
• How to Follow Up on Unpaid Invoices
• Best Invoicing Software for Tutors

Frequently Asked Questions

What features should virtual assistants look for in invoicing software?

Recurring invoices for retainers, time tracking that turns hours into invoice lines, online card and bank payments, and automatic reminders. Check each feature on the vendor's own pages before you sign up.

How should a virtual assistant invoice a retainer with extra hours?

Bill the retainer and the extra hours as separate lines. In this page's sample, a $900.00 retainer for 20 hours plus 6.5 extra hours at $45.00 comes to $1,192.50.

Which of these tools track time?

Billed, FreshBooks and Zoho Invoice each describe time tracking on their own pages, and each describes turning tracked time into an invoice.

Can the other tools on this page track the retainer hours that remain?

Among the other tools on this page, FreshBooks describes dedicating a specific number of hours to a client's retainer and scheduling work against that amount. Check each tool if you need this.

How much does invoicing software for virtual assistants cost?

This page doesn't list prices because they change. Check each vendor's pricing page, and include payment processing fees and any per-user charges in your comparison.