Shopify Agencies

Shopify Agency Management Software for Builds, Plus, and Growth Retainers

Run phased Shopify and Shopify Plus store builds, track Liquid customization separately from app configuration, manage catalog migrations, and convert launched stores into recurring growth retainers — all in one merchant-facing platform.

TL;DR for Shopify Agency Owners

AgencyPro replaces the duct tape most Shopify agencies run on — Asana or ClickUp for tasks, HoneyBook for proposals, QuickBooks for invoicing, GitHub for theme code, Slack for chaos — with one merchant-facing platform built for store builds and growth retainers.

→Phased Shopify and Shopify Plus build templates with development store and live store URLs in the portal.
→Time tracking that separates Liquid dev, app block work, app configuration, catalog migration and theme editor setup.
→Pass-through billing for Klaviyo, Recharge, Yotpo, Gorgias and the rest of the app stack.
→Monthly growth retainers with hour pools, CRO experiment tracking and performance reports pulled from Shopify analytics.
→Higher rates for Plus-specific work (checkout extensibility, Functions, B2B, Markets) tracked separately for profitability reporting.

From Store Build to Merchant Growth — Simplified

Stop juggling spreadsheets and scattered communication. AgencyPro centralizes Shopify and Shopify Plus builds, Liquid workflows, app pass-through and growth retainers so you can deliver more stores and retain more merchants.

Shopify Store Build Phases with Plus Support

Structure each store build into the phases your team actually delivers: discovery, theme selection or design, Liquid development, app installation and configuration, product import, payment and shipping setup, QA on a development store, and launch. Shopify Plus engagements get extra phases for checkout customization, Functions/Scripts, B2B configuration and multi-store setup.

Liquid Theme Customization & App Block Tracking

Track time separately across the layers Shopify work actually involves — Liquid template editing, section schema customization, app block configuration, custom theme sections, metafield setup, custom CSS/JS injections, theme editor configuration. Spotting which layer consumed 40% of your last build hours is how you stop underquoting the next one.

Merchant Portal with Store-Specific Context

Every merchant gets a branded portal that links directly to their development store URL, their live store, and their phase of work. Merchants who own multiple Shopify stores see them rolled up. Internal team sees full context; merchants see what matters to them — phase status, staging links, invoices, and the next decision they need to make.

Product Import & Catalog Migration Hours

Catalog work eats Shopify agency margins more than any other line item. Product CSV mapping, metafield creation, image optimization, SEO redirects from the old store, variant mapping, inventory cleanup — log each separately so the merchant pays for the work that actually happened. Big migrations from Magento, WooCommerce or BigCommerce get their own phase.

Build Pricing + Growth Retainer Billing

Most Shopify agencies run two billing motions: a fixed-price (or phased) build for the initial launch, and a monthly growth retainer afterward covering theme updates, app management, CRO experiments, seasonal campaign work and Shopify Plus support. AgencyPro handles both, plus pass-through billing for the apps you install on the merchant's behalf.

Store Performance & CRO Reporting

Pull Shopify analytics — sessions, conversion rate, average order value, repeat customer rate — into a monthly merchant report. Pair it with the work you shipped that month. Merchants who can see "we ran two A/B tests and conversion went from 1.6% to 2.1%" renew their retainer. Merchants who only see the invoice question it every quarter.

A Shopify Store Build from Discovery Through Growth Retainer

Follow a typical store build through eight gates — discovery, design, Liquid dev, catalog, apps, QA, launch and handoff — with billing and merchant communication built into each transition.

Discovery & Plus Qualification

Scope the merchant's catalog size, traffic, GMV, integrations and growth plans. Decide whether they need standard Shopify or Shopify Plus, and configure the build template accordingly.

Design Direction or Theme Selection

Custom design in Figma, or pick and customize from the Shopify Theme Store. Document brand decisions and approve direction before any Liquid is written.

Development Store & Liquid Build

Spin up the development store, build sections, configure app blocks, write custom Liquid where the theme falls short, set up metafields and dynamic sources.

Product Import & Catalog Setup

Map product CSV from the old store or PIM, configure variants and inventory, set up collections, install SEO redirects from the legacy URLs, optimize product imagery.

App Integration & Payment Configuration

Install and configure required apps (reviews, subscriptions, loyalty, email, shipping, ERP) with merchant-billed pass-through. Configure Shopify Payments, alternative gateways, taxes and shipping zones.

QA, Soft Launch & Production Cutover

Run order tests on the dev store, validate checkout flows, audit speed and accessibility, do a soft launch to a small audience, monitor for 48 hours, then full launch.

Merchant Training & Handoff

Record Shopify admin training videos, walk the merchant through the new theme editor configuration, deliver brand assets and content guidelines through the portal.

Convert to Growth Retainer

Propose a monthly retainer covering theme updates, app management, seasonal campaign builds, CRO experiments and Shopify Plus support. First retainer invoice fires the month after launch.

Shopify Agencies Delivering Faster, Retaining Longer

Top Shopify partners use AgencyPro to manage store builds, separate Plus revenue from standard Shopify revenue, and improve merchant retention through recurring growth retainers.

✓

Stop Underquoting Catalog Migrations

Migration work is notoriously hard to estimate. Tracking past CSV mapping, metafield setup and redirect mapping hours gives you defensible quotes for the next migration from Magento, WooCommerce or BigCommerce.

✓

Convert Build Clients into Retainer Revenue

A launched store is the easiest retainer pitch you will ever make. Use the build data, the launch metrics and the growth roadmap to propose a $1,500-$8,000/mo retainer the week after go-live.

✓

Pass Through App Subscriptions Cleanly

Stop eating $30/mo on Klaviyo, $200/mo on Recharge or $500/mo on Yotpo. Configure pass-through billing once; the apps appear on the merchant invoice every month with your margin baked in.

✓

Separate Plus Work from Standard Shopify Work

Shopify Plus engagements (checkout extensibility, Functions, Scripts, B2B, Markets) command higher rates. Track them separately so you know which Plus features are profitable and which silently absorb hours.

✓

Make CRO a Renewable Service Line

A/B tests, conversion experiments and seasonal campaign builds become recurring retainer line items with attached performance data. Merchants who see "test A lifted AOV by 11%" do not cancel.

✓

Manage Multi-Store Merchants Without Losing Track

Brands with three regional Shopify stores, or a Shopify Plus merchant running five sub-brands, get a parent merchant view with per-store projects rolling up.

Faster

Store builds

2.5x

Faster merchant payments

$1,800

Avg monthly retainer captured per launched store

Based on average results reported by agencies using AgencyPro

Four Shopify Agency Engagement Patterns

Most Shopify agencies recognize themselves in one of these four shapes. AgencyPro handles all four with the same data model — what changes is the build template and the retainer structure.

DTC brand launch ($15k-$40k fixed price)

A direct-to-consumer brand launching with 50-300 SKUs on standard Shopify. Theme Store theme with brand customization, 8-12 apps configured (Klaviyo, Recharge, Yotpo, etc.), launch in 4-8 weeks.

How AgencyPro fits: Use the standard Shopify build template. 50% deposit, 30% at dev store walkthrough, 20% at launch. Convert the merchant to a $1,500-$2,500/mo growth retainer the week after launch.

Shopify Plus replatform ($80k-$250k)

A scaling brand or enterprise migrating from Magento, BigCommerce or a custom stack to Shopify Plus. Custom theme, checkout extensibility, Functions for tax or shipping logic, multi-currency, ERP integration. Project runs 4-7 months.

How AgencyPro fits: Plus build template with extra phases. Higher Plus rates for checkout, Functions and Markets work. Catalog migration gets its own phase. Post-launch retainer is typically $5k-$15k/mo covering ongoing Plus support and CRO.

Theme refresh + CRO retainer

A brand 12-24 months post-launch wants a theme refresh and an ongoing CRO program. Smaller fixed-price project ($8k-$25k) followed by a $3k-$8k/mo CRO retainer with A/B tests and conversion experiments.

How AgencyPro fits: Mini-build template for the theme refresh. CRO retainer template with monthly experiment log, performance reports pulled from Shopify analytics, and an experiment library the merchant can review.

Growth retainer for an established brand

An established Shopify or Shopify Plus merchant doing $5M-$50M+ GMV who needs an ongoing partner for theme updates, seasonal campaigns, app management, and feature work. No build to start, just a long retainer.

How AgencyPro fits: 40-80 hour monthly retainer with hour pool tracking. Merchant submits requests through the portal; tickets log against the pool; quarterly business reviews use the data to defend the rate or expand the scope.

The Shopify Agency Tool Stack AgencyPro Replaces

Most Shopify agencies grew up with a stack stitched together from project tools meant for marketing agencies, proposal tools meant for freelancers, and a Slack channel per merchant. Here is the typical setup and what AgencyPro takes off the plate.

Current tool	What it does today	AgencyPro replacement
Asana / ClickUp / Monday	Project tasks, internal team coordination	Native projects with Shopify and Shopify Plus build templates
HoneyBook / Dubsado / Bonsai	Proposals, contracts, deposits	Proposals, e-signed contracts, milestone deposits all native
QuickBooks / Xero	Invoicing, accounting	Invoice from AgencyPro; sync to QuickBooks/Xero for the books
Slack (merchant channels)	Merchant chat, status updates, feedback	Structured comments in the portal so nothing dies in DMs
GitHub / theme repos	Liquid theme source control, GitHub Shopify integration	Keep entirely; link theme repos and Shopify GitHub deploys from the portal
Notion / Google Drive	SOWs, training docs, credentials	SOWs, training videos, credentials vault all per-merchant
Shopify Partner dashboard	Development stores, partner billing, referrals	Keep entirely; link dev and live store URLs from the AgencyPro merchant portal

Pricing Math for an 8-Person Shopify Agency

List prices for an 8-person Shopify Partner running roughly 4 active builds and 15 growth retainers.

Tool	Configuration	Monthly cost
Asana Business	8 seats x $24.99	$200
ClickUp Business+ (alt)	8 seats x $19	$152
HoneyBook	Per team essential plan	$79
QuickBooks Online Plus	Per organization	$99
Slack Business+	8 seats x $15	$120
GitHub Teams	8 seats x $4	$32
Stack total (typical)	Six separate vendors	~$530 - $682/mo
AgencyPro Agency tier	Replaces Asana, HoneyBook, portal layer, doc storage	$199/mo

Keep GitHub and the Shopify Partner dashboard. Sunset Asana/ClickUp, HoneyBook and the patchwork portal. The bigger lift comes from making catalog migration time billable, separating Plus rates from standard rates, and capturing pass-through margin on apps.

Migrating from Your Current Shopify Agency Stack

Most Shopify agency migrations take 3-7 days of part-time work. Here is the piece-by-piece breakdown.

From Asana or ClickUp

Export active builds and retainers via CSV. Map to AgencyPro merchant records and apply the appropriate Shopify or Shopify Plus build template. Most agencies only use 4-6 custom fields in Asana; recreate those once and migrate in one afternoon.

From HoneyBook or Dubsado

New proposals get drafted in AgencyPro from now on. Active in-flight proposals finish out in HoneyBook to avoid disruption. The proposal templates port over in about an hour each — most agencies have 2-4 templates total.

From QuickBooks invoicing

Stop generating invoices in QuickBooks. Generate in AgencyPro; sync to QuickBooks via the native integration so accounting still has the data. Most agencies cut over at the start of a calendar month.

From Slack merchant channels

Keep Slack for internal team chat. Move structured merchant communication — feedback, approvals, change requests — into portal comments so it does not get lost in a #merchantname-acme channel that no one searches later.

Is AgencyPro Right for Your Shopify Agency?

AgencyPro is built for Shopify and Shopify Plus agencies running multi-phase store builds and ongoing growth retainers. Here is when it fits and when another tool is a better choice.

AgencyPro might NOT be the right fit if:

•You're a solo Shopify expert with 1-3 merchants. HoneyBook, Bonsai or Dubsado handle invoicing without the platform overhead.
•You're a 100+ person enterprise Shopify Plus shop. Workamajig, Kantata or Mavenlink integrate with finance and resource planning at enterprise scale.
•You only need a Shopify-specific PM tool. Tools that integrate directly with Shopify Partner dashboards may fit better if you want store-level data inside your PM tool.
•You only customize themes with no time tracking. A simpler invoicing tool plus a basic project tracker may be enough for single-deliverable theme work.
•Your work is one-off store launches with no retainers. A pure project-based tool may serve you better if you don't need monthly retainer cycles.

AgencyPro is a great fit if:

•You run a Shopify agency with 5-50 active builds and retainers. Phase-based billing, time tracking and merchant portals across all engagements without spreadsheets.
•Mid-build scope creep eats your margin. Track scope changes against original quotes and surface chargeable overages before launch.
•You bill across project, milestone and ongoing growth retainer. One platform handles all three instead of juggling separate tools for builds and retainers.
•You need a merchant-friendly client portal. Branded portal gives merchants status, deliverables and invoices without learning your internal tools.
•You want margin data per phase (theme, integration, CRO). Discover which work types drive profit and price future quotes based on real data.

Price Your Next Shopify Build or Growth Retainer

Most Shopify agencies leave money on the table by underpricing the catalog phase and the post-launch retainer. Run your last build through the project profitability calculator and price your next retainer with the retainer pricing calculator.

Retainer Pricing Calculator →Project Profitability Calculator →

Frequently Asked Questions

Get answers to common questions about our platform.

How does AgencyPro handle the difference between Shopify and Shopify Plus engagements?

Standard Shopify builds use a 7-phase template (discovery, design, theme dev, catalog, apps, QA, launch). Shopify Plus builds extend that template with checkout extensibility, Functions and Scripts setup, Launchpad configuration, B2B catalog setup, Markets configuration and multi-store coordination — and you can apply higher Plus-specific billing rates to those phases. The merchant portal adapts to show whichever scope applies.

Can I track Liquid development time separately from app configuration time?

Yes, and you should. Track Liquid template work, section schema customization, app block configuration, app settings configuration, metafield setup and theme editor configuration as separate categories with their own rates. Most agencies discover Liquid work earns the highest effective rate while app configuration is often underbilled. The data lets you reprice.

How does the product import and catalog migration workflow work?

Catalog migration gets its own phase with its own hour budget. Log time against CSV mapping, image optimization, variant configuration, metafield population, SEO redirect mapping and inventory reconciliation. For migrations from Magento, WooCommerce or BigCommerce, the template includes the platform-specific gotchas (e.g. WooCommerce variation product imports, Magento attribute set translation) so you do not rediscover them every time.

How do I pass through Shopify app subscriptions to merchants?

Configure each app with its monthly cost, your markup, and the merchant who pays for it. The recurring invoice line items appear on the merchant's monthly retainer or as a separate apps line. Common pass-throughs: Klaviyo, Recharge, Yotpo, Judge.me, Loop, Postscript, Gorgias, Searchanise. Margin on apps becomes a real revenue line instead of a leakage point.

How does milestone billing work for fixed-price Shopify builds?

Configure the build with milestones tied to phases — kickoff deposit, design approval, dev store walkthrough, soft launch and full launch are common breakpoints. Marking the milestone complete fires the invoice with a summary of what shipped in that phase. Merchants pay through the portal via Stripe or ACH; payment status flows back to the build automatically.

How do I structure a growth retainer after the store launches?

Most Shopify agencies sell retainers in 10-hour, 20-hour or 40-hour monthly buckets covering theme updates, app management, seasonal campaigns, CRO experiments and Plus support. Configure the retainer once; the monthly invoice fires automatically; merchant requests log against the hour pool with overage detection at 80% usage. Quarterly reviews use the data to justify renewals or upgrades.

Can merchants see store performance data in their portal?

Yes. Pull session count, conversion rate, AOV, repeat customer rate and revenue from Shopify into a monthly merchant report. Pair it with the work you shipped that month. The combination — what you did + what happened — is what gets retainers renewed. Merchants who only see invoices renegotiate every quarter; merchants who see results re-up annually.

How does AgencyPro handle multi-store and headless commerce merchants?

Multi-store merchants (one brand running US, UK and EU storefronts) get a parent merchant record with per-store projects underneath. Headless commerce builds (Hydrogen, Next.js + Storefront API, custom React) get their own template since the work composition is different — more frontend, less Liquid, more API integration. The same engagement and billing logic applies regardless of architecture.

Does AgencyPro integrate with the Shopify Partner dashboard?

AgencyPro is a client-facing operating system; it does not try to replace the Shopify Partner dashboard. You still manage development stores, billing relationships and partner referrals in the Partner dashboard. AgencyPro handles everything client-facing — proposals, portals, time, milestones, invoicing, retainers — and links to the live and dev store URLs through the portal.

How does AgencyPro support Shopify Plus features like Functions and Scripts?

Plus-specific work (checkout extensibility, Functions, Scripts, B2B catalogs, Markets configuration, Launchpad) gets tagged in the project so you can report on Plus revenue separately from standard Shopify revenue. Use higher billing rates for Plus-specialized engineers, and configure templates so Plus engagements never get scoped at standard Shopify hours.

A Realistic Scenario: 6-Person Shopify Plus Agency

Picture a 6-person Shopify Plus agency working with mid-market DTC brands. Two senior Liquid developers, one frontend engineer, one designer, one merchant success manager, one founder. Around three active builds in the $40k-$150k range at any time, plus a roster of 18 growth retainers between $1,500 and $8,000 per month.

Before: ClickUp for projects, HoneyBook for proposals, QuickBooks for invoicing, Slack channels per merchant, GitHub for theme code, a shared Google Drive for everything else. The founder spends Sunday nights consolidating the retainer invoices for the 1st. App pass-through revenue disappears because no one tracks it consistently. The agency suspects it could be charging more for Plus work but does not have the data to prove it.

After 90 days on AgencyPro: ClickUp is gone. HoneyBook is gone for new business (active proposals finish out where they started). All 18 retainer invoices fire on the 1st automatically with hour-pool usage summaries attached. App pass-through is configured for Klaviyo, Recharge, Yotpo, Gorgias and Loop across the merchant base — adding roughly $2,100/mo in previously absorbed margin.

Where it actually moves the business: Phase-level reporting on the last six builds reveals that Plus checkout customization averaged 2.3x the original estimate while standard Liquid theme dev was tracking close to plan. The agency raises its Plus checkout rate by 35% on the next two proposals and adjusts the scoping template to allocate more discovery time to checkout edge cases. The next Plus build clears its target margin for the first time in a year. That single repricing decision pays for the AgencyPro subscription roughly 70 times over for the year.