TLDR (Summary)
The best invoicing software for agencies is Plutio ($19/month).
Agencies billing clients for project work and retainer hours need invoicing that connects to time tracking and sends professional invoices with detailed breakdowns. Plutio generates invoices from logged time, processes payments through Stripe and PayPal, and follows up on overdue invoices automatically.
SPI Research shows billable utilization has dropped to 68.9% as admin burden increases. Connected invoicing eliminates manual time-to-invoice handoffs.
What is invoicing software for agencies?
Invoicing software for agencies is software that creates professional invoices from tracked time and project milestones, processes payments, and manages recurring billing for retainer clients.
The distinction matters: basic invoicing creates bills, agency invoicing connects to the operational data (time tracked, projects delivered, retainer allocations) that determines what to bill.
What agency invoicing actually does
Core functions include generating invoices from time tracking data, creating milestone invoices for project-based work, managing recurring invoices for retainer clients, processing online payments, tracking payment status, and sending reminders for overdue amounts.
Accounting software vs agency invoicing
accounting software and Leading bookkeeping tools excel at bookkeeping but require manual invoice creation. Agency invoicing tools like Plutio connect to operational data: time entries become invoice line items, project milestones trigger billing, retainer usage generates monthly invoices. The billing data already exists in the work.
What makes agency invoicing different
Agencies have complex billing: project milestones, hourly work, retainer allocations, sometimes all for the same client. Monthly billing runs involve pulling data from multiple sources and calculating what each client owes. Connected invoicing automates this entirely.
When invoicing connects to time tracking and projects, billing becomes a review step rather than a data assembly project. Time logs contain what to bill; invoicing just formats and sends it.
Why you need invoicing software
Agencies without proper invoicing lose revenue to delayed billing, spend excessive time on invoice preparation, and struggle with cash flow from late payments.
The billing delay problem
Research shows agencies spend several hours weekly on billing when it isn't connected to time tracking. Payment delay pushes billing later, extending payment cycles and hurting cash flow.
What breaks without proper invoicing
- Billing delays: Manual preparation pushes invoices out later than work completion
- Data errors: Transferring time data manually creates calculation mistakes
- Missed hours: Time logged but not included on invoices means unbilled work
- Cash flow gaps: Late invoicing plus late payment creates extended cash cycles
- Collection burden: Manual follow-up on overdue invoices consumes account manager time
The retainer complexity
Retainer clients require tracking hours used versus allocated, billing for overages, potentially rolling over unused hours, and documenting usage on invoices. Without connected systems, this requires spreadsheet tracking and manual invoice construction each month.
Connected invoicing transforms billing from an administrative burden to a quick review. Time tracking already contains the data; invoicing just presents it professionally and collects payment.
Invoicing features agencies need
The essential invoicing features for agencies handle complex billing scenarios while connecting to time tracking and enabling fast payment collection.
Core invoicing features
- Professional templates: Branded invoices that look professional and reflect your agency
- Time-based billing: Generate invoices directly from time tracking entries
- Milestone billing: Invoice at project milestones based on deliverables
- Online payments: Accept credit cards and bank transfers instantly
- Payment reminders: Automated follow-up on overdue invoices
- Partial payments: Accept deposits and split payments
Agency-specific features
- Retainer billing: Monthly invoices showing hours used versus allocated
- Overage handling: Automatic calculations for hours beyond retainer allocation
- Recurring invoices: Automatic monthly billing for retainer clients
- Multi-project invoicing: Combine charges from multiple projects on one invoice
Platform features that multiply value
- Client portals: Clients view and pay invoices through branded portals
- Payment processing: Stripe and PayPal integration for immediate payment
- Reporting: Revenue, outstanding amounts, and payment trends
- Accounting integration: Sync to accounting software or Leading bookkeeping tools for bookkeeping
The deciding factor for agencies is time tracking connection. Invoicing that pulls from logged hours eliminates the most time-consuming step of billing preparation.
Invoicing software pricing for agencies
Invoicing software for agencies typically costs $15-60 per month, with pricing often based on features or invoice volume rather than users.
What agencies typically pay for stacked tools
You piece together multiple subscriptions:
- Invoicing: Standard billing software ($17-55/month), accounting software ($30-90/month), Leading bookkeeping tools ($15-70/month)
- Time tracking: standalone timers ($12/user), time tracking software ($10-20/user)
- Payment processing: Transaction fees (2.9% + $0.30 typical)
A growing agency spends $100-300/month on invoicing and the time tracking it needs to connect to.
Plutio pricing (January 2026)
- Core: $19/month - Complete invoicing with time tracking, projects, CRM, and payment processing
- Pro: $49/month - Unlimited clients, 30 team contributors, advanced permissions, priority support
- Max: $199/month - Unlimited contributors, advanced reporting, white-label portals
The ROI calculation for agencies
If connected invoicing saves 5 hours weekly of admin time:
- Time saved: 5 hours/week of admin time recovered
- Monthly savings: $800/month in recovered admin capacity
- Tool cost: $19-99/month
- Additional value: Faster billing, faster payment, better cash flow
Invoicing ROI comes from admin time saved plus faster payment collection. Both directly impact cash flow and operational efficiency.
Why Plutio is the best invoicing software for agencies
Plutio handles invoicing as part of a complete platform where proposals, contracts, projects, time tracking, and clients communication work together rather than as separate tools that need manual connection.
Complete workflow integration
When a client accepts your proposal, Plutio can automatically create the project, set up the invoicing schedule based on milestone payments, and prepare the contract for signing. When they sign, setup tasks generate. When you track time on agency work, those hours attach to the project. When a milestone completes, the action triggers. Every step connects to the next without copying data between systems.
White-label everything
Use your own domain (clients.yourstudio.com instead of plutio.com/yourusername). Upload your logo, set your brand colors and typography. Every client-facing touchpoint shows your brand: proposals, contracts, invoices, portals, emails, receipts. clients never see "Plutio" or any indication you're using third-party software. Brand perception matters for agencies because professional appearance affects perceived value and justifies premium pricing.
Unified inbox for all clients communication
When a client messages about a campaign, responds to a proposal, approves work, or asks about billing, the message appears in one inbox. Reply directly without opening email. The conversation history stays attached to that client's record, so months later when they return, you have full context.
Granular permissions
Control exactly who sees what at the level that makes sense for your business. Contractors see only their assigned work. clients see their portal and documents. Neither sees your internal notes, profit margins, or other clients data.
No-code automations
Create rules that trigger actions without your involvement. Common agencies automations include: send reminders before due dates, notify you when a client views a proposal, create follow-up tasks when items are overdue, send welcome emails when contracts are signed. Set up once during initial configuration, runs continuously without attention.
Native integrations for agencies workflows
Connect Stripe and PayPal for payments with no additional configuration. Sync Google Calendar or Outlook for scheduling. Add Zoom links to booked calls automatically. Push financial data to accounting software or Leading bookkeeping tools for accounting. Use Zapier to connect 3,000+ other apps. Plutio handles the core workflow while integrating with specialized tools where deeper functionality is needed.
Partial payments and payment plans
Accept deposits, milestone payments, and payment plans. Track partial payments against invoice totals automatically. When clients need flexibility, you can accommodate without losing track of what's owed.
Multi-currency support
Invoice international clients in their preferred currency. Plutio handles conversion and displays amounts correctly for each client. Expand your agency's reach without invoicing complications.
Expense tracking and pass-through billing
Log expenses against projects and clients. Mark expenses as billable to include them on invoices automatically. Pass through costs for stock photos, software subscriptions, or contractor fees without manual tracking.
Everything runs from one app with your branding, your terminology, and your workflow logic. Instead of switching between 5-8 different tools to manage one client, you operate from a single platform designed to handle the complete service business lifecycle.
Automated Payment Reminders
Set up automatic payment reminders that go out before and after due dates. Customize the tone and timing to match your client relationships while keeping consistent follow-up on outstanding balances.
Multi-Currency Support
Bill international clients in their preferred currency while tracking revenue in yours. Plutio handles exchange rates and keeps your financial reporting clean regardless of where your clients are located.
Revenue Recognition Tracking
Track when income is earned versus when it's billed for accurate financial reporting. See outstanding receivables, upcoming payments, and cash flow projections all in one dashboard.
Expense Tracking Integration
Attach billable expenses directly to projects and include them on client invoices automatically. Track reimbursable costs from receipt to payment without manual data entry or lost documentation.
Invoice Templates
Design branded invoice templates that match your agency's identity. Include custom payment terms, bank details, and terms of service that reinforce your professional image with every billing cycle.
Partial Payment Handling
Accept and track partial payments on large invoices. See remaining balances at a glance and send appropriate follow-ups for outstanding amounts without manual calculation or confusion about what's been paid.
Batch Invoice Generation
Generate multiple invoices at once for recurring client work or retainer billing. Set billing schedules that automatically create invoices on your chosen dates, saving hours of repetitive invoice creation.
Late Fee Management
Configure automatic late fee policies that apply consistently across overdue invoices. Maintain clear payment expectations while preserving client relationships.
How to set up invoicing in Plutio
Setting up invoicing in Plutio takes 30-60 minutes for initial configuration, with invoices ready to send immediately after.
Step 1: Configure invoice settings (15-20 minutes)
Set up your invoice defaults:
- Invoice numbering: Prefix and sequence for invoice numbers
- Payment terms: Default due date (Net 15, Net 30, etc.)
- Tax settings: Tax rates if applicable to your services
- Default notes: Payment instructions, thank you message
Step 2: Connect payment processing
Link Stripe, PayPal, or both for payment acceptance. Configure which methods appear on invoices. Set up bank account for payout deposits.
Step 3: Customize invoice template
Add your logo, adjust colors to match your brand, configure which fields appear. Preview how invoices will look to clients.
Step 4: Set up reminder schedules
Configure automatic reminders for overdue invoices:
- First reminder: Day after due date
- Second reminder: 7 days overdue
- Third reminder: 14 days overdue
Step 5: Send your first invoice
Create an invoice from time entries or manually. Review, send, and watch the workflow in action.
Start with defaults and refine based on client feedback. Payment terms and reminder schedules can adjust as you learn what works for your client base.
Invoice templates for agencies
Different billing scenarios require different invoice approaches. Configure templates that match your engagement types.
Recommended invoice templates for agencies
- Time-based invoice: Detailed hour breakdown by date and task
- Project milestone invoice: Deliverable-based billing at project stages
- Retainer invoice: Monthly recurring with hours used/remaining
- Mixed invoice: Combines retainer hours plus additional project work
- Deposit invoice: Upfront payment before project start
Invoice components
- Header: Your logo, contact info, invoice number, date
- Client info: Client name, address, billing contact
- Line items: Services, descriptions, quantities, rates
- Summary: Subtotal, taxes if applicable, total due
- Payment: Terms, methods, instructions
- Footer: Thank you message, late payment policy
The level of detail depends on client expectations. Some want every hour itemized; others prefer deliverable summaries. Configure templates that match relationship needs.
Client portals for invoicing
A client portal gives clients branded access to their billing history and a simple way to pay outstanding invoices.
What clients see in billing portals
Configure client visibility based on your preferences:
- Current invoices: Outstanding amounts requiring payment
- Payment history: All past invoices and payment records
- Time details: Hours logged that will appear on upcoming invoices
- Retainer status: Hours used and remaining on current allocation
Reducing payment friction
When clients pay through portals, they click one button to access invoice, another to pay. No downloading PDFs, no finding payment links in emails. Reduced friction means faster payment collection.
Self-service access
Clients who need invoices for their own accounting can access them anytime. No emailing requests for copies of past invoices. Everything lives in their portal.
Building payment habits
Regular portal access for project status creates habits that extend to billing. Clients who check their portal regularly notice and pay invoices faster than those who only receive emails.
Portals transform billing from push communication to pull access. Clients engage with invoices on their terms, in their branded portal, when convenient for them. Payment history becomes immediately visible, reducing questions about past transactions. When clients need receipts or documentation for their own records, self-service access eliminates requests that would otherwise interrupt your workflow and consume valuable team administrative time on routine billing and client payment tasks
How to migrate invoicing to Plutio
Migrating invoicing involves setting up new workflows and handling any outstanding invoices in the transition. You complete migration in 1-2 weeks.
Step 1: Set up Plutio invoicing (30-60 minutes)
Configure settings, connect payment processing, customize templates. Complete setup before transitioning from old system.
Step 2: Decide on transition approach
Options for the transition:
- Clean cutoff: New invoices in Plutio, existing outstanding in old system until paid
- Immediate migration: Recreate any unpaid invoices in Plutio, cancel in old system
- Date-based split: All work after a certain date bills through Plutio
Step 3: Handle outstanding invoices
For unpaid invoices in old system:
- Keep in old system until paid, then close account
- Or recreate in Plutio with same numbers for continuity
Step 4: Update client expectations
If payment methods or processes change, notify clients. Provide portal access if new to them. Brief email explaining what's different.
Step 5: Run parallel briefly if needed
Keep old system accessible (read-only) until confident in new workflow. You fully transition within 2-4 weeks.
Accounting continuity matters for reporting. Decide whether to recreate historical invoice data or let old system serve as archive for past records.
