Invoicing Software for E-Commerce Agencies
E-commerce agencies manage diverse invoicing: one-time store setup and development projects, ongoing product management retainers, and marketing campaign work. AgencyPro automates e-commerce invoicing by tracking setup, development, product management, and marketing separately, so you bill accurately for each service while managing retainer-based product management alongside project work.
Based on self-reported data from AgencyPro customers
Built for E-Commerce Agencies
E-commerce agencies bill a tangled mix of platform build fees, monthly optimization retainers, and performance bonuses tied to revenue targets — each requiring a different invoicing cadence and calculation. When the Shopify build is billed at project milestones, the CRO retainer runs monthly, and the performance bonus triggers only when revenue exceeds targets, three billing clocks run simultaneously for a single client.
Invoicing Built for E-Commerce Agencies
Why E-Commerce Agencies Need Better Invoicing
Agencies building and managing online stores, marketplaces, and digital commerce solutions.
The Shopify build was a $45K project, but now the client pays a $4K monthly retainer for product management — and your invoicing still treats everything as one continuous engagement with no clear transition point
Shopify subscription fees, Klaviyo charges, premium theme licenses, and app costs all pass through to the client, but they're buried in your service invoice making your agency fees look inflated
A client's retainer covers product catalog updates and basic CRO, but they keep requesting "quick" feature additions that take 6-8 hours each — and nobody invoices the overage because it's awkward mid-retainer
Revenue-share billing triggers when the store exceeds a monthly GMV target, but calculating the agency's percentage against Shopify's analytics dashboard and reconciling with actual payouts takes hours each month
How E-Commerce Agencies Use AgencyPro Invoicing
Professional invoicing with time-to-invoice automation, multiple payment gateways, and branded invoice delivery.
Project-to-retainer transitions happen cleanly: the final build milestone closes the project invoice, and the first monthly retainer invoice starts on the agreed date with its own scope definition and billing terms
Platform and app costs appear in a dedicated "Technology Costs" section on every invoice — Shopify Plus at $2,300/mo, Klaviyo at $850/mo, and ReCharge at $300/mo all itemized separately from your $4,000 service retainer
Retainer scope tracking flags when accumulated out-of-scope requests exceed a threshold you set, automatically generating a supplemental invoice for overages rather than absorbing them into next month's retainer
Performance billing pulls store revenue data and applies your agreed percentage above the GMV threshold — if the deal is 5% of revenue above $200K/mo and the store did $340K, your $7,000 performance fee calculates and invoices automatically
Key Benefits for E-Commerce Agencies
Store Build vs. Optimization Billing
Separate one-time e-commerce store setup and development invoices from ongoing conversion rate optimization and product management retainers.
Platform & App Cost Pass-Through
Itemize Shopify, WooCommerce, or BigCommerce platform fees, premium app subscriptions, and payment gateway costs separately from agency service fees.
Product Management Retainer Invoicing
Auto-generate monthly invoices for product catalog management, inventory updates, product photography, and listing optimization.
Revenue Share & Performance Billing
Support performance-based billing models where agency fees are tied to store revenue milestones, alongside traditional hourly or retainer invoicing.
How It Works
Separate build milestones from retainer billing
The store build invoices at agreed milestones: 30% at kickoff, 30% at staging review, 40% at launch. Post-launch, the retainer billing schedule activates with its own scope, rate, and cadence — no overlap, no confusion.
Pass through platform costs transparently
Enter Shopify, app, and third-party tool costs each month. AgencyPro adds them as itemized pass-throughs on the client invoice, clearly separated from your service fees. Markup rules apply per cost category if your contracts include technology management fees.
Track retainer scope and bill overages
Each retainer defines included hours and service scope. When a client requests work outside the retainer (new feature build, migration, redesign), those hours accumulate in a separate bucket and invoice as project work at your standard rate.
Frequently Asked Questions
The store launched last month and the client is transitioning from build to retainer. How do we handle this?
Close the build project with a final milestone invoice covering the launch deliverables. Then activate the retainer billing on the agreed start date — first of next month, 30 days post-launch, whatever the contract says. AgencyPro keeps the two billing tracks separate so there's no overlap period where the client gets charged for both a build milestone and the first retainer month.
Our retainer includes 20 product uploads per month, but the client sent 45 this month. How do we bill the overage?
Set the retainer scope to include 20 uploads. When the team logs product upload work beyond that threshold, AgencyPro flags the overage and accumulates it in a separate billable bucket. At month-end, the retainer invoice goes out as normal, plus a supplemental invoice for 25 additional uploads at your per-upload rate. The client sees exactly where they exceeded scope.
We manage Shopify apps and subscriptions on behalf of the client. Can we pass those through with a management fee?
Yes. Enter each app subscription (Klaviyo, ReCharge, Yotpo, etc.) with the actual cost and your management markup. The invoice shows the app cost and your fee as separate columns — Klaviyo $850 + $150 management fee. Clients see exactly what the tool costs versus what they pay you to manage it, and you capture revenue for the real work of configuring and maintaining their tech stack.
How does performance-based billing work when our fee is a percentage of store revenue?
Define the revenue threshold and your percentage. Each month, enter the store's GMV (or connect your analytics). AgencyPro calculates your performance fee — if the agreement is 4% above $150K and the store did $280K, your fee is $5,200. The invoice shows the calculation formula, revenue data source, and resulting fee. Combined with your base retainer, the client sees both the fixed and variable components of your compensation.
Invoicing for Other Industries
Invoicing Software for Marketing Agencies
Digital and traditional marketing firms managing campaigns, content, and strategy for multiple clients.
Invoicing Software for SEO Agencies
Search engine optimization firms tracking rankings, building links, and optimizing websites for organic traffic.
Invoicing Software for PPC Agencies
Pay-per-click agencies managing Google Ads, Meta Ads, and multi-platform paid advertising campaigns.
Invoicing Software for Social Media Agencies
Agencies managing social content, community engagement, and social advertising across platforms.
Invoicing Software for Content Agencies
Content marketing firms producing blogs, whitepapers, video scripts, and editorial content for brands.
Invoicing Software for PR Agencies
Public relations firms managing media outreach, crisis communications, and brand reputation.
More AgencyPro Solutions for E-Commerce Agencies
Time Tracking Software for E-Commerce Agencies
Smart time tracking with project-level timers, billable/non-billable categorization, and team timesheets.
Client Portal for E-Commerce Agencies
Branded client-facing portal for project updates, file sharing, approvals, and transparent communication.
Project Management Software for E-Commerce Agencies
Agency-focused project management with task boards, deadlines, team assignments, and client collaboration.
CRM Software for E-Commerce Agencies
Client relationship management built for service businesses with deal pipeline, contact management, and client lifecycle tracking.
Reporting & Analytics Software for E-Commerce Agencies
Real-time dashboards and automated reports covering revenue, profitability, utilization, and project performance.
Recurring Billing Software for E-Commerce Agencies
Automated subscription and retainer billing with payment processing, dunning management, and revenue recognition.
The build is done. Don't let recurring revenue slip through the cracks.
E-commerce agencies using AgencyPro capture 20% more recurring revenue by automating the build-to-retainer transition. Platform pass-throughs, scope overages, and performance fees all invoice on schedule.