TLDR (Summary)
The best invoicing software for bookkeepers is Plutio ($19/month).
Bookkeeping practices need invoicing that connects to time tracking and automates recurring billing. Plutio converts logged hours to invoice line items, sends recurring invoices automatically, and provides client portals for payment and history access.
Bookkeepers using Plutio create invoices faster by eliminating manual data entry and automating recurring client billing. According to research, 36% of goes to administrative tasks that connected invoicing eliminates.
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What is invoicing software for bookkeepers?
Invoicing software for bookkeepers is software that handles billing and payment collection, tracks status, sends automated notifications, and connects invoicing directly to engagements.
The distinction matters: basic tools handle one function in isolation, while bookkeepers-focused invoicing software combines multiple functions while connecting to project management, clients communication, and workflow automation.
What bookkeepers invoicing software actually does
Core functions include creating branded templates with your logo and colors, setting up recurring workflows for retainer clients, converting tracked work into billable items, handling different engagements types, sending automated reminders at intervals you choose, and providing clients with a branded portal. Advanced platforms add workflow automation where completed steps automatically trigger the next action.
Standalone invoicing vs integrated platforms
standalone applications like other tools, accounting software, Legacy invoicing apps handle invoicing as an isolated function. You enter client details manually, create items from scratch, and track status in a separate system from your engagements. Integrated platforms like Plutio connect invoicing with proposals, contracts, projects, time tracking, and clients communication. When you finish a engagement, Plutio already knows the scope, the tracked hours, and the client's history.
What makes bookkeepers invoicing different
Bookkeepers face unique scenarios that generic invoicing software struggles with: milestone billing; retainers; hourly projects; and engagements scope that can shift mid-engagement. Without invoicing that connects to engagements status, the process becomes disconnected from the work itself.
Bookkeepers engagements also range dramatically in value. A small engagement and a large one both need invoicing, but the structure, schedule, and follow-up sequence differ completely. Invoicing software built for bookkeepers handles these variations through templates rather than manual setup each time.
When invoicing connects to projects, contracts, and time tracking, the manual copying between apps disappears. Changes update everywhere automatically, and invoicing reflects what actually happened instead of what you remember to enter.
Why bookkeepers need invoicing software
Bookkeepers who grow beyond a handful of active clients face a compounding problem: every new client adds admin work that does not scale, and automated invoicing and payment reminders is where that admin tends to pile up.
Lead tracking, quoting, billing, payment follow-ups, and clients communication multiply with each engagement. Without a system that connects these functions, details fall through cracks, invoicing tasks accumulate during busy engagements phases, and Spending evenings catching up on admin instead of resting or doing bookkeeping work.
The late payments problem
According to industry research, 36% admin. For bookkeepers specifically, that means 10-15 hours per week spent on non-billable tasks: late payments, manual invoice creation, payment tracking, and responding to clients questions.
Those 10 hours of admin represent significant potential billable time that goes unbilled. That's thousands per month in opportunity cost, not counting the mental energy spent on context switching between bookkeeping work and administrative tasks.
The fragmentation problem
You stack 4-7 disconnected tools: QuickBooks or Xero for accounting, FreshBooks or Wave for invoicing, spreadsheets for tracking, and email for client communication. Each tool handles one function, but none share data automatically.
Disconnected tools create daily friction: logging into multiple platforms to piece together a client's history, copying details from one system to another, manually cross-referencing entries with project scope, and hoping that the terms you quoted match what you're actually delivering. The cognitive admin work adds up, and the risk of errors increases with every manual handoff.
The manual invoice creation epidemic
Manual invoice creation affects nearly every bookkeeper at some point. According to research, 50-70% experience, with the average invoice paid 20 days.
The issue compounds because bookkeepers often work on multiple engagements with different schedules. Manual tracking across spreadsheets or disconnected tools leads to missed tasks, forgotten follow-ups, and opportunities left on the table.
The scaling tipping point
You hit a threshold where the manual approach breaks down. At this point, you're either spending more time on admin than bookkeeping work, or you're dropping balls. Tasks go out late, follow-ups get missed, and you start turning down good work because you can't imagine adding more complexity to an already chaotic system.
Connected invoicing software absorbs the admin work that would otherwise scale linearly with each new client. Plutio handles routine invoicing tasks, tracking, and follow-ups automatically, leaving bookkeepers to focus on the work that actually generates revenue.
Invoicing features bookkeepers need
The essential invoicing features for bookkeepers connect billing and payment collection with engagements delivery, time tracking, and clients communication while handling the unique patterns that bookkeeping work requires.
Core invoicing features
- Custom templates: Add your logo, brand colors, typography, and terms. Create different templates for milestone billing, retainers, hourly projects. Set up once and apply with one click.
- Multiple payment methods: Accept credit cards through Stripe (2.9% + $0.30 per transaction), bank transfers via ACH (typically 0.8%), or PayPal. Offering multiple options increases completion speed.
- Automated reminders: Configure reminders before due dates, on due dates, and after. Follow-ups send automatically without you drafting messages or remembering to check status.
- Recurring automation: Schedule recurring tasks for retainer clients that send automatically on set dates. Pair with automation to complete without either party taking action.
- Time-to-billing conversion: Select tracked time entries from engagements and convert directly to billable items. No copying hours from a time tracker. The description, duration, and rate pull automatically.
- Expense tracking: Log engagements expenses with receipts attached. Add to clients billing at cost or with markup (common practice is 10-15%).
Bookkeepers-specific features
- Deposit collection: Request upfront payment before work begins. Industry standard is 25-50% deposit. Plutio should connect deposits to final billing automatically.
- Milestone billing: Split engagements payment across phases. Each milestone triggers its own action when you mark that phase complete.
- Revision tracking: When scope expands beyond contracted revisions, the billing should reflect additional work. Connect revision logs to billing so extra rounds generate accurate charges.
- Proposal-to-project flow: When a client accepts a proposal, the schedule should generate automatically based on the payment terms defined.
Platform features that multiply value
- White-label branding: Custom domain, logo, colors, and fonts. All clients-facing communications show your brand. clients never see the software vendor's name.
- Unified inbox: All clients messages, engagements comments, and notifications arrive in one place. Reply without switching to email. Conversation history stays attached for context.
- Permissions: Control who sees what. Contractors see only their assigned work. clients see their portal, not your internal notes or margins.
- Customizable navigation: Rename menu items to match how you talk about your work. Hide features you don't use to reduce clutter.
- Mobile apps: iOS and Android apps for full functionality on the go. Work from anywhere with the same capabilities as desktop.
- Automations: Create rules that trigger actions without your involvement. Set up once, runs continuously.
The deciding factor for bookkeepers is integration depth. Invoicing software that connects with proposals, contracts, projects, time tracking, and clients communication eliminates the duplicate data entry that consumes hours every week.
Invoicing software pricing for bookkeepers
Invoicing software for bookkeepers typically costs $15-50 per month for standalone tools, with practice platforms including invoicing in broader packages.
What bookkeepers typically pay for stacked tools
Most practices piece together multiple subscriptions:
- Invoicing: Standard billing software ($15-50/month), accounting software ($25-80/month)
- Time tracking: time tracking software ($10-20/user), standalone timers ($12/user)
- Payment processing: Stripe (2.9% + 30¢), PayPal (2.9% + 30¢)
A 3-person practice spends $100-200/month on invoicing plus time tracking.
Plutio pricing (January 2026)
- Core: $19/month - Complete invoicing with time tracking, projects, and CRM
- 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 bookkeepers
If connected invoicing saves 5 hours monthly on billing administration:
- Time saved: 5 hours x $50/hour = $250/month
- Faster collections: Days-earlier payment improves cash flow
- Tool cost: $19-99/month for entire practice
Invoicing ROI comes from eliminated billing time plus faster payment collection. Both directly impact practice cash flow.
Why Plutio is the best invoicing software for bookkeepers
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 bookkeeping 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 bookkeepers because professional appearance affects perceived value and justifies premium pricing.
Unified inbox for all clients communication
When a client messages about a engagement, 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 bookkeepers 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 bookkeepers 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.
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.
How to set up invoicing in Plutio
Setting up invoicing in Plutio takes 30-60 minutes, with professional invoices ready to send immediately after configuration.
Step 1: Configure invoice settings (15-20 minutes)
Set up your billing foundation:
- Practice information: Name, address, tax ID
- Payment terms: Default due dates (Net 15, Net 30)
- Tax settings: Applicable tax rates
- Invoice numbering: Prefix and sequence
Step 2: Configure branding
Set up your invoice appearance: logo placement, brand colors, custom messaging. Consistent professional presentation across all invoices.
Step 3: Connect payment processing
Set up payment acceptance:
- Stripe: Credit card processing
- PayPal: PayPal payment acceptance
- Bank details: For direct transfer payments
Step 4: Set up recurring invoices
Configure automatic billing for retainer clients. Set amounts, schedules, and delivery timing.
Step 5: Send your first invoice
Create from time entries or from scratch. Send through portal or email. Monitor view and payment status.
Start with manual invoices to verify settings. Add recurring automation once billing workflow is confirmed. Build systematically.
Invoice templates for bookkeepers
Different billing arrangements benefit from different invoice structures. Configure templates for common scenarios.
Invoice type templates
- Time-based: Detailed hourly breakdown with descriptions
- Fixed-fee: Monthly retainer amount with service summary
- Project: Milestone-based billing with progress notes
- Combined: Retainer base plus hourly overage
Standard invoice sections
- Header: Your branding, client details, invoice number
- Line items: Services, quantities, rates, amounts
- Summary: Subtotal, taxes, total due
- Footer: Payment instructions, terms, thank you message
Recurring invoice schedules
- Monthly retainers: Generate 1st of month, due 15th
- Quarterly: Generate beginning of quarter
- Annual: Engagement renewal billing
Templates make sure consistent billing presentation. Every client receives professional invoices without per-invoice formatting effort.
Client portals for invoice delivery
Client portals provide a branded destination for invoice delivery, payment, and billing history access.
Invoice accessibility
Current and historical invoices appear in client portals. Clients access their billing anytime without contacting you. Download for records. Pay directly.
Payment convenience
Pay buttons right on invoices. Click to pay by card or bank transfer. No separate payment portals. Smooth payment experience improves collection speed.
Billing history
Complete invoice history by client. See all past invoices, payment dates, and amounts. Self-service access to billing records.
Reducing payment friction
The easier you make payment, the faster you get paid. Portal access with one-click payment removes barriers between invoice receipt and payment completion.
Portal invoice delivery creates professional billing experience. Clients appreciate easy access and convenient payment. You appreciate faster collection.
How to migrate invoicing to Plutio
Migration from another invoicing software typically takes 3-5 hours of active work spread over a weekend, with the best time to switch being between engagements rather than mid-delivery when you have active clients commitments.
Step 1: Export from your current tool
Most invoicing software provides CSV export for clients data and document archives. Here's what to export from common tools:
- Standard billing software: Export clients and engagements data from Settings or Reports. Download important documents manually.
- accounting software: Export contacts and history from Reports section. Download transaction history for reference.
- Legacy invoicing apps: Export clients list and engagements data. Use the data export feature for complete records.
Step 2: Build templates in Plutio (2-3 hours)
Use your exported content as reference to create new templates. Start with the engagement type you use most frequently. Recreate 2-3 core templates initially rather than trying to migrate every document you've ever created. Focus on forward-looking workflows, not historical archives.
Step 3: Set up integrations (30 mins)
Connect payment processing (Stripe, PayPal), calendar sync (Google Calendar, Outlook), and accounting software (accounting software, Leading bookkeeping tools). Test each integration with a sample transaction to make sure data flows correctly before relying on it for real clients work.
Step 4: Import clients data (30 mins)
Upload your clients CSV to Plutio. Map fields appropriately (name, email, company, phone, address). For active clients with ongoing engagements, create their records. For historical clients you may never work with again, consider whether import is necessary.
Step 5: Run parallel for new work
Use Plutio for all new clients engagements while keeping the old system active for engagements already in progress. Running parallel avoids the complexity of migrating mid-engagement work and gives you time to learn the new system on fresh engagements. As active engagements on the old system complete, those clients transition to Plutio for future work.
Step 6: Phase out the old tool
Once all active engagements on your old system complete (typically 30-60 days), cancel that subscription. Maintain read-only access to historical records if the tool allows, or export final archives before cancellation.
Common migration pitfalls to avoid
- Trying to migrate everything: Focus on active clients and forward-looking workflows. Historical data can remain in archives.
- Switching mid-engagement: Finish in-progress work on the old system. Start new clients on Plutio.
- Not testing integrations: Verify payment processing works with a real (small) transaction before relying on it.
- Skipping the learning curve: Use the first 2-3 engagements as deliberate learning opportunities.
The investment in migration pays back in time saved on every future engagement, proposal, and clients interaction. Plan for a weekend of setup and a few weeks of adjustment, then benefit from simplified workflows going forward.
