Best Automated Invoicing Software

Explore invoicing and payment solutions built around how your industry bills. Law firms collect retainers, consultation fees, and monthly statements by card; CPA and bookkeeping practices bill engagement fees, tax-season returns, and monthly bookkeeping; outsourced CFOs bill a roster of small-business clients; and distributors, contractors, healthcare practices, property managers, and subscription businesses invoice on their own cycles. Clearwater Processing combines automated invoicing with card payment acceptance, recurring billing, a virtual terminal, QuickBooks and Xero integration, and a dedicated representative so firms spend less time chasing receivables.

Business owner reviewing automated invoices and online payment activity on a laptop

Automated Invoicing by Industry

Automated invoicing and payment workflows built for how each industry bills, from law firms, CPA and bookkeeping practices, and outsourced CFOs to wholesale distributors, contractors, healthcare practices, property managers, and subscription businesses.

Law Firm Retainers & Consultation Fees

Invoice initial retainers, consultation fees, and monthly statements for hourly work, send a replenishment request when an evergreen retainer runs low, and let clients pay by card online or over the phone, so collections don’t wait on mailed checks.

Monthly Bookkeeping & Advisory Fees

Put fixed-fee bookkeeping, advisory, and fractional CFO engagements on back-office recurring billing; once a client authorizes a card, the monthly fee is collected on schedule instead of invoiced and chased, while one-off cleanup or catch-up projects can still be invoiced separately. Clearwater can automatically update a client’s card on file before it expires, so the monthly charge keeps running without staff stepping in.

Payments That Post to QuickBooks or Xero

Connect client payments to QuickBooks or Xero so the firm’s paid invoices close out against the right client and matter in its own books with less manual entry, leaving fewer open receivables to chase down before month-end. Using the same client and matter references on the invoice and in the books keeps that matching automatic as the client list grows.

Card Payments Taken by Phone or Email

When a client calls with a card to settle an invoice or a past-due balance, billing staff key it into the virtual terminal during the call, so the card number never ends up on a sticky note or in an email.

Engagement & Milestone Invoices

Bill tax-return preparation, audits, case phases, and project-based advisory work as each milestone is reached, such as a deposit when the engagement letter is signed and the balance before a return is released for e-filing, with clients paying online through a secure ecommerce gateway that accepts all major card types.

Payment Reporting for the Firm

Review transaction details and merchant statements in the secure Merchant Reporting Portal to see which engagement invoices and monthly fees have been paid, and use statement analysis to spot hidden fees in what the firm pays to accept client cards.

Scheduled Invoices & Pay-by-Card Links

Set recurring engagement invoices, monthly statements, and retainer replenishment requests to go out on a fixed schedule, with a secure pay-by-card link on each one so the client can settle from the email instead of mailing a check. Pair those links with the firm’s own reminder schedule, such as a courtesy note before the due date and a follow-up after it, and check the Merchant Reporting Portal to see which invoices have been paid before reminders go out.

Dual Pricing & Surcharge Programs

Clearwater Processing’s custom invoicing supports dual pricing and zero-fee (surcharge) programs, so a firm can show a card price and a check or ACH price on the invoice, or pass card costs to clients who choose to pay by card. Programs are set up only where card-network rules, state law, and any professional conduct rules that apply to the firm allow them, with the fee disclosed before the client pays.

Wholesale & B2B Distributor Invoicing

Invoice business accounts on net terms with a secure pay-by-card link on every invoice, and key orders or past-due balances phoned in by a buyer into the virtual terminal. Payments post to QuickBooks or Xero against the right customer account, and where card-network rules and state law allow, dual pricing or surcharge programs help offset the cost of accepting cards on larger invoices.

Contractor & Field Service Invoices

Bill a deposit before materials are ordered, progress payments as each phase is finished, and the balance at the final walkthrough. Customers can pay from the emailed invoice link, crews can take a card on site with a standalone EMV terminal, and the office can key phone payments into the virtual terminal, so jobs close out without waiting on a check.

Patient Statements for Healthcare Practices

Send medical, dental, and specialty patients statements for the balance left after insurance, with a secure link to pay by card online. Front-desk staff can take payments by phone through the virtual terminal, and larger balances can be set up as recurring payment plans, with cards that are about to expire updated automatically so plan payments keep coming in.

Rent, HOA Dues & Assessments

Bill monthly rent, HOA dues, and special assessments on a recurring schedule, let residents and owners pay by card online, and automatically update expiring cards so recurring dues keep collecting. Parent and sub-parent reporting lets a management company review each property or association on its own and see its whole portfolio together.

Subscription & SaaS Billing

Charge monthly or annual plans automatically through back-office recurring billing or the ecommerce gateway’s API, invoice usage, add-ons, and setup fees separately, and keep revenue from lapsing with automatic updating of customer cards that are about to expire. Developers can test the integration in a sandbox account before going live.

Industry-Specific Invoicing

Automated Invoicing Built Around How Your Industry Bills

Every industry bills in its own pattern, and generic invoicing tools don’t always fit. A law firm may collect a consultation fee at intake, take a retainer before work begins, and send monthly statements as hours accrue, often keeping retainer deposits separate from payments for earned fees. A CPA practice bills engagement fees, sees invoices pile up between February and April, and carries extension work into the fall, while a bookkeeping firm charges the same fee every month. Outsourced CFOs bill monthly fees across many small-business clients, with separate project invoices for budgets, forecasts, or lender packages. Outside professional services, the patterns change again: a wholesale distributor invoices business accounts on net terms, a contractor bills a deposit, progress payments, and a final balance, a medical or dental practice sends patient statements for what insurance didn’t cover, a property manager collects monthly rent, HOA dues, and assessments, and a subscription business charges the same plan every cycle. Across all of them, the same collections problem repeats: invoices that sit unpaid for weeks because paying means writing and mailing a check. Clearwater Processing matches each pattern with the right tools: custom invoices customers can pay by card online or by phone, back-office recurring billing, a virtual terminal for keyed payments, standalone EMV terminals for payments taken on site, QuickBooks and Xero integration for reconciliation, next-day funding, and a dedicated representative with industry experience you can reach on a direct cell phone number. Automation is what keeps that from becoming a second job for the billing staff. With automated invoicing software, recurring invoices and monthly statements go out on a set schedule instead of being rebuilt each cycle, every emailed invoice carries a secure link the customer can use to pay by card, and payments post back to the business’s accounting software so no one has to match deposits to invoices by hand. For customers on recurring charges, Clearwater Processing can also automatically update cards on file that are about to expire, so a retainer, bookkeeping fee, patient payment plan, HOA dues payment, or subscription keeps charging without a call to the customer and the business keeps that revenue. Where card-network rules, state law, and any professional rules that apply allow it, Clearwater’s custom invoicing supports dual pricing and zero-fee (surcharge) programs, and businesses with more than one office, location, or property can review payment activity through parent and sub-parent reporting.

Digital invoicing dashboard showing customer payments and transaction reporting
The Clearwater Difference

Why Choose Clearwater Processing?

Clearwater Processing pairs payment technology with invoicing setups built around each industry’s billing cycle and the accounting systems businesses already rely on.

Industry Experience

Merchant-services experience behind processing setups for businesses whose billing mixes retainers, net-terms invoices, deposits and progress payments, and recurring charges.

Personal Support

A single point of contact, a real person with industry experience rather than a call center, reachable on a personal cell number, plus U.S.-based backend phone support 24/7/365, including the late nights before filing deadlines and month-end close.

Fee Visibility

Statement analysis deciphers every line item on a firm’s processing statement, so partners can see what accepting card-paid invoices costs, with clients seeing average savings of 10%–30%.

Built for Client Billing

Scheduled invoices clients can pay by card, recurring billing with automatic updating of expiring cards, keyed phone payments, and QuickBooks or Xero integration configured for professional firms, distributors, contractors, healthcare practices, property managers, and subscription businesses.

Meet The Clearwater Team

Experienced payment specialists help professional firms, distributors, contractors, healthcare practices, property managers, and subscription businesses set up how their customers are invoiced and pay by card.

Since opening in 2003, Clearwater Processing has tailored processing environments to each merchant and grown into a broader payment-services provider, led by executives with decades of experience in credit card processing and merchant services. Its capabilities include ecommerce gateways, back-office billing, standalone terminals, PCI compliance solutions, merchant statement analysis, reporting, funding, and personalized support. Clearwater Processing maintains locations in South Florida, New York City, and Arizona while serving clients in 32 states across the United States. For each industry, representatives focus on the business’s own billing cycle: retainers and engagement invoices, net-terms wholesale invoices, contractor deposits and progress payments, patient statements, monthly dues, and subscriptions. The company’s approach combines payment technology with direct communication, transparent merchant guidance, and dedicated representatives who help businesses understand processing activity and select solutions suited to their operational needs.

EstablishedServing merchants since 2003
CoverageServing clients in 32 states
SupportU.S.-based backend support 24/7/365

Frequently Asked Questions

What is the best automated invoice processing software?

The best setup is the one that fits how the business already bills and keeps its books. A law firm taking retainers, a CPA practice working through tax season, a wholesale distributor invoicing on net terms, a contractor billing deposits and progress payments, a medical practice sending patient statements, a property manager collecting monthly dues, and a subscription business charging the same plan every cycle each need different things from invoicing and payments. Clearwater Processing offers custom invoicing with card payment acceptance, pay-by-card links, recurring billing with automatic card updating, a virtual terminal, QuickBooks and Xero integration, merchant reporting, PCI compliance support, and a dedicated representative, so the payment environment can be matched to the existing workflow.

How can law firms take retainer and consultation payments by card?

How do CPA firms keep up with tax-season billing?

Can bookkeeping firms bill monthly fees without sending a new invoice?

Can customers pay invoices by credit card?

How do outsourced CFO firms bill their fees across many small-business clients?

What payment options can a firm offer its clients?

Does automated invoicing software support online payments?

How can a firm understand what it pays to process client payments?

What support is available during tax season and month-end close?

How does automated invoicing software reduce late payments for professional firms?

Can retainers and monthly fees keep charging when a client’s card expires?

Can a firm add a card fee to client invoices?

Can a firm with several offices see all of its invoice payments in one place?

What should a firm check before connecting invoicing to its accounting software?

How do wholesale and B2B distributors use automated invoicing?

Can contractors collect deposits and progress payments with automated invoices?

How can medical and dental practices automate patient billing?

Can property managers and HOAs automate rent and dues collection?

Does automated invoicing work for subscription and SaaS businesses?

Need Help Choosing An Invoicing Solution?

Talk with Clearwater Processing about your industry’s billing cycle and accounting workflow.

Ready To Simplify Client Billing?

Tell Clearwater Processing how your business bills, whether retainers, net-terms wholesale invoices, contractor deposits, patient statements, monthly dues, or subscriptions, and discuss a processing environment that fits your industry.

Contact Us Today

For immediate assistance, feel free to give us a direct call at 973-715-5416.