TL;DR for Web Development Agency Owners
AgencyPro replaces the seven-tool stack most web agencies cobble together — Asana for tasks, Linear or GitHub Issues for the engineering team, Harvest for time, QuickBooks for invoicing, Slack for chaos, Notion for documents and one of three random tools for client portals.
- →Track time by phase (discovery, design, frontend, backend, QA, launch) and by role at different billing rates.
- →Drop staging URLs into the portal; clients leave page-pinned comments on Vercel, Netlify or self-hosted preview links.
- →Milestone-triggered invoicing — mark a phase done, the invoice fires.
- →Convert every launched build into a monthly maintenance retainer with hour caps and overage tracking.
- →Pricing starts at $99/mo for the agency tier — typically replaces $500-$900/mo of subscriptions.
Website Builds Organized by Phase, Billed by Milestone
Site builds follow a predictable arc: discovery, wireframes, design, frontend, backend, QA, launch. AgencyPro tracks hours per phase and role, shares staging links for review, and triggers invoices at each completion gate.
Most generic PM tools assume a flat task list. Web builds do not work that way. AgencyPro structures each project into the five phases your agency actually delivers — discovery, design, frontend, backend, QA and launch — and shows completion percentage, open blockers and remaining budget per phase. Engineers see what is next; account managers see what is at risk; clients see clear progress without learning your stack.
Log time against tagged categories — HTML/CSS markup, React or Vue component work, API integration, server-side logic, database modeling, cross-browser QA, accessibility passes, performance tuning. After three or four projects you can pull a report that says "our last five marketing sites averaged 38% frontend, 27% backend, 14% QA," then use that distribution to quote the next one with confidence.
Drop a staging URL (dev.client.com, staging.client.com, a Vercel preview link, a Netlify deploy) into a project phase and give the client read access. Clients leave comments tied to specific pages instead of sending a Slack message that says "the hero feels off." Each staging deployment is timestamped so everyone knows which version they are reviewing.
Most web shops bill 30% deposit, 30% at design approval, 30% at development complete, 10% at launch — and chase every payment manually. AgencyPro generates the invoice the moment you mark a milestone complete, with a summary of what shipped in that phase. Clients pay through the portal; QuickBooks or Xero sync handles the bookkeeping.
After launch, every bug fix, content tweak and small feature ask becomes a tracked support ticket — not a Slack favor. Hours roll up against a monthly maintenance retainer cap. When a client burns through their 10 hours by the third week, the system flags it and either prompts an overage invoice or a retainer upgrade conversation, with the evidence already attached.
A pre-launch checklist (DNS, SSL, analytics, sitemap, robots.txt, redirects, 404 pages, performance audit, accessibility audit) keeps the engineering team honest. Credentials, CMS training videos, hosting documentation and brand guidelines go into a per-client vault so the next person to touch the site — agency or client side — is not starting from zero.
A Website Build from Discovery to Maintenance Retainer
Follow a typical site project through eight gates — discovery, wireframes, design, frontend, backend, QA, launch and handoff — with time tracking and payment collection at every transition.
Discovery & Sitemap
Run stakeholder calls, document goals and constraints, build a sitemap and content inventory, agree on the tech stack (Next.js + headless CMS, WordPress + Elementor, custom Node stack) and confirm phase-level pricing.
Wireframes & Design Comps
Produce low-fidelity wireframes for key templates, then high-fidelity comps in Figma. Share comps in the portal for written approval; design approval is the trigger for the second milestone invoice.
Frontend Build on Staging
Implement the design system, build templates, wire up animations and responsive states. Deploy continuously to staging.dev.clientname.com and tag each deployment with the phase it represents.
Backend, CMS & Integrations
Set up the CMS (Sanity, Contentful, WordPress headless), build any custom APIs, integrate analytics, marketing automation and form handlers, configure caching and CDN.
QA, Accessibility & Performance
Run cross-browser testing, Lighthouse audits, WCAG 2.1 AA checks, broken-link scans, redirect maps for the legacy site. Log every fix against the QA bucket.
Client Review Cycle on Staging
Send the staging link with a structured review checklist. Collect page-pinned comments, batch the revisions, communicate which feedback is in scope and which is a change order.
Launch, DNS Cutover & Smoke Test
Push to production behind a feature flag, swap DNS, monitor uptime, run a smoke test of the top 20 pages, file the final milestone invoice and trigger the retainer paperwork.
Handoff & Maintenance Retainer Kickoff
Record CMS training videos, deliver credentials and documentation through the portal, schedule a 30-day post-launch review and start tracking the first month of retainer hours.
How Phase-Level Tracking Improves Web Build Margins
Web development agencies that track hours by build layer and bill per milestone collect payments faster, quote future projects more accurately, and recover revenue from mid-build change orders.
Know Exactly What Frontend vs. Backend Costs
Separate time tracking by development layer reveals whether your sites are frontend-heavy or backend-heavy. Use this data to adjust quotes for similar future projects.
Collect Progress Payments Without Chasing Clients
Phase-gated invoices trigger automatically when you mark a milestone complete. Clients receive the invoice with a summary of what was delivered in that phase.
End Staging Confusion with Version-Labeled URLs
Each staging deployment is labeled with its phase and date. Clients know exactly which version they are reviewing and what changed since the last deployment.
Bill Mid-Build Feature Requests Separately
When a client asks for a new page or interactive feature mid-build, log it as a change order. The system tracks hours against the original scope versus additions.
Quote Future Builds Using Past Build Data
Historical time per build phase (design, frontend, backend, QA) gives you accurate benchmarks. A 10-page corporate site takes X hours — you have the data to prove it.
Transition Smoothly from Build to Maintenance
After launch, convert the project into a monthly retainer with maintenance hour caps. Post-launch support time is tracked separately from the original build budget.
Avg time from milestone to payment
Estimates vs. actuals
Avg recovered from mid-build change orders
Based on average results reported by agencies using AgencyPro
Four Common Web Development Agency Scenarios
The shape of your work changes how you should configure the platform. Here are the four most common engagement patterns we see and how AgencyPro handles each.
Custom marketing-site build ($25k-$80k fixed price)
10-30 page Next.js or WordPress build for a Series A or B company. Tight launch date tied to a fundraise announcement or product launch. Stakeholders include a CMO, a designer client-side and an internal dev who will own the site after launch.
How AgencyPro fits: Use the 30/25/30/10/5 milestone template. Set up frontend, backend, design and PM time categories. Share staging on Vercel preview URLs. The 5% milestone fires 30 days after launch to cover post-launch fixes — and naturally opens the retainer conversation.
Headless commerce build ($60k-$200k)
Next.js frontend + Shopify or commerce.js backend, custom checkout, multi-region pricing, integrations with a PIM, a CRM and a 3PL. Build runs 3-5 months with significant backend complexity.
How AgencyPro fits: Switch to T&M billing in two-week sprints or hybrid (fixed price for scoped phases, hourly for integrations). Track frontend, backend, integration, QA and DevOps as separate categories so you can see exactly where the build is overrunning. Use the change order workflow when the PIM scope inevitably grows.
Ongoing dev retainer for a SaaS product ($8k-$25k/month)
You are functioning as a fractional engineering team for a venture-backed startup. Two-week sprints, weekly demos, mix of feature work, bug fixes and infrastructure projects.
How AgencyPro fits: Set up a monthly retainer with an hour pool. Sprint goals live in the project; daily time logs roll up against the pool. The client portal shows sprint-by-sprint output and remaining hours. When a feature ask blows past the sprint capacity, the change order workflow makes it a billable extension instead of free overtime.
Care plan for a small business roster (15-40 clients)
You have a pipeline of small WordPress, Webflow or custom-built sites and you charge $200-$1,000 per month for monthly updates, content changes, security and uptime. The pain is operational, not technical.
How AgencyPro fits: Templatize the care plan as a recurring monthly invoice with a 2-5 hour pool. Clients submit requests through the portal; tickets log against their pool; overage hours either bill immediately or roll into a separate change order. The reporting tells you which clients are profitable and which are eating 12 hours for a 3-hour fee.
The Web Development Agency Tool Stack AgencyPro Replaces
Most established web dev agencies arrive at AgencyPro with the same Frankenstein stack: a PM tool for tasks, an engineering tool for tickets, a time tracker, an invoicing tool, an accounting tool, a chat tool and a docs tool — plus a half-broken client portal stitched together with Notion shares and shared Google Drives.
| Current tool | What it does today | AgencyPro replacement |
|---|---|---|
| Asana / Monday / ClickUp | Project tasks, client-facing project view | Native projects + phase milestones with branded client portal |
| Linear / Jira / GitHub Issues | Engineering ticket queue, sprint cycles | Keep for engineering tickets; sync milestone status into AgencyPro |
| GitHub / GitLab / Bitbucket | Source control, PR reviews | Keep entirely; share staging URLs and release notes through portal |
| Harvest / Toggl / Clockify | Time tracking across projects | Built-in time tracking by phase, role, billable status, rate |
| QuickBooks / Xero / FreshBooks | Invoicing, accounting, expense tracking | Invoicing + Stripe/ACH payments; sync to QuickBooks/Xero for books |
| Slack / shared inbox | Client back-and-forth, status updates | Threaded client comments on phases and staging URLs; Slack for team |
| Notion / Google Drive | Proposals, SOWs, documentation, credentials | Proposals + SOWs + credentials vault + handoff docs per client |
Pricing Math for a Typical 10-Person Web Dev Agency
These numbers are based on published list prices for a team of 10 with around 20 active client engagements. Your exact total varies; the pattern does not.
| Tool | Configuration | Monthly cost |
|---|---|---|
| Asana Business | 10 seats x $24.99 | $250 |
| Linear Business | 10 seats x $14 | $140 |
| Harvest | 10 seats x $13.75 | $138 |
| QuickBooks Online Advanced | Per organization | $235 |
| Slack Business+ | 10 seats x $15 | $150 |
| Notion Business | 10 seats x $18 | $180 |
| Client portal add-on or custom build | Varies wildly | $0-$300 |
| Stack total | Seven separate vendors | ~$1,093 - $1,393/mo |
| AgencyPro Agency tier | Replaces 5 of 7 above + adds portal | $199/mo |
Keep Linear and GitHub for engineering; sunset Asana, Harvest, the client portal add-on and the Notion-as-CRM hack. Net subscription savings typically land at $600-$900 per month on top of the recovered admin hours.
Migrating from Your Current Web Dev Stack
Most migrations land in under a week of part-time effort. Here is what each one looks like.
From Asana or Monday
Export active projects via CSV. Map projects to AgencyPro clients and phases. Recreate any custom fields you actually use (most agencies only need 3-5). Keep Asana read-only for two weeks while you cut over — by the third week it is gone.
From Harvest or Toggl
Export historical time data for the last 90 days for reporting continuity. Start new timers in AgencyPro from day one — there is no need to backfill. Configure rate categories before the team logs the first hour to avoid mid-month re-coding.
From QuickBooks or Xero
Keep QuickBooks/Xero as your accounting system of record. Send invoices from AgencyPro; sync them into QuickBooks via the native integration. Stop using QuickBooks for invoice generation — its templates are not why you bought it.
From a custom client portal
Most custom portals are read-only Notion shares or a basic Laravel app no one wants to maintain. Move active clients to AgencyPro portals one at a time, send them a 90-second video walkthrough, and decommission the legacy portal once the last client logs into the new one.
Is AgencyPro Right for Your Web Development Agency?
AgencyPro is built for web development agencies running multi-phase builds with client portals, milestone billing and ongoing maintenance 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 developer with 1-3 retainer clients. Bonsai, Harvest, or HoneyBook handle the basics without an agency platform.
- •You're a 100+ person enterprise dev shop. Kantata, Mavenlink, or Workamajig are designed for the resource planning and finance integration enterprise dev firms require.
- •You need deep technical PM features (Jira/Linear). AgencyPro is for client-facing ops, not engineering ticket management. Pair it with Linear or Jira for the dev team.
- •Your team uses GitHub Projects exclusively for client work. If your engagement model is fully developer-led with no PM layer, AgencyPro may add overhead you don't need.
- •You only build with one productized package and Stripe. A simpler queue tool plus Stripe Subscriptions might be enough.
AgencyPro is a great fit if:
- •You run a dev agency with 5-50 active builds and retainers. Phase-based billing, time tracking and client portals across all engagements without rebuilding spreadsheets every month.
- •Mid-build change orders never get billed. Track scope changes against original estimates and surface chargeable overages before launch.
- •You bill across project, milestone and maintenance retainer. One platform handles all three rather than juggling separate invoicing and project tools.
- •You need a client portal for non-technical stakeholders. Branded portal lets clients see status, deliverables and invoices without learning Linear or GitHub.
- •You want margin data per build phase. Discover which build phases (discovery, design, dev, QA, launch) are underpriced and adjust quotes for future projects.
Calculate the True Cost of Your Last Web Build
Most web agencies feel they are underpriced but cannot prove it. Plug your last project into the Project Profitability Calculator — actual hours, blended rate, overhead, change orders — and see whether the build cleared 40% gross margin or quietly ate the team alive.
Frequently Asked Questions
Get answers to common questions about our platform.
How does AgencyPro handle the discovery, design, dev, QA and launch phases of a web build?
Each web project is structured as a parent record with five phase children — discovery, design, frontend/backend dev, QA, launch. Tasks, time entries and deliverables attach to a phase. Phase completion is a one-click action that triggers the milestone invoice, posts a status update to the client portal and unlocks the next phase. You can also add custom phases (content migration, third-party integration, accessibility remediation) for projects that need them.
Can I track frontend, backend and DevOps hours at different billing rates?
Yes. Each time-tracking category has its own billing rate. A typical web dev agency configures senior frontend at one rate, mid-level frontend at another, senior backend higher, DevOps higher still, QA lower, account management at an internal rate. When you generate an invoice, the system rolls up hours by rate so the client sees a clean line-item summary instead of one big block of "developer time."
How does staging URL sharing actually work day-to-day?
Drop the staging URL into the project (vercel preview, Netlify deploy, your own staging.client.com, even a password-protected dev environment). The client gets read access through their portal, opens the link, and leaves page-pinned comments. Each new deploy gets its own timestamped row so the client can compare what changed since their last review. Internal-only deploys stay hidden from the client view.
What happens when a client asks for a new feature mid-build?
Log it as a change order against the project. The system records the request, the estimate, the client approval and the eventual hours. At launch you have a clean record showing original scope hours vs. additions, which makes the final reconciliation invoice impossible to argue with. Agencies typically recover $2,000-$5,000 per project from change orders they used to absorb silently.
How does milestone billing work for fixed-price web projects?
You define the milestones up front in the proposal (e.g. 30% deposit, 25% at design approval, 30% at dev complete, 10% at launch, 5% at 30-day post-launch). Each milestone is tied to a deliverable. Marking the milestone complete generates the invoice with a short summary of what shipped in that phase. Clients pay through the portal via Stripe, ACH or wire; the payment status flows back to the project automatically.
How do I move a client from build to a maintenance retainer without dropping the ball?
At launch, generate a retainer proposal from a template (hours per month, scope inclusions, response time SLA, monthly price). The client signs in the portal, the first recurring invoice fires, and the project pivots from build mode to retainer mode. Post-launch tickets get logged against the retainer hour pool; when 80% of the pool is used in a given month, the system flags it so you can have an upgrade conversation before you eat the overage.
Can I customize the client portal for non-technical stakeholders?
Yes. Brand it with your logo, colors and custom domain. Hide the engineering-only sections (commit history, ticket details, internal notes) and show only what the client cares about — phase status, staging links, deliverables, invoices, support requests. The same project has a full-detail view for your team and a clean executive view for the client.
How does AgencyPro scale from a 3-person shop to a 30-person agency?
There is no per-user fee cliff that punishes growth, and the data model is the same whether you have five projects or fifty. As you grow you turn on resource planning (who is allocated where for the next four weeks), pipeline forecasting (what is in proposal stage and likely to land), and team utilization reports (which roles are over/under capacity). The client-facing experience stays consistent across team size.
Does AgencyPro replace Linear, Jira or GitHub for the engineering team?
No. AgencyPro is the client-facing layer — proposals, portals, time, milestones, invoicing. Engineering teams keep using Linear, Jira or GitHub Projects for ticket-level work and pull requests. Most agencies wire AgencyPro to those tools so that completing a Linear cycle or merging a release PR can update the milestone status. You get developer-grade tooling for the team and account-manager-grade tooling for the client.
How does AgencyPro handle both project-based work and ongoing retainers in one platform?
Each client can have any mix of fixed-price builds, time-and-materials sprints and monthly retainers running at the same time. The dashboard rolls them up so you can see total active revenue per client, profitability across engagement types, and which clients are net positive after everyone logs their hours honestly. No more juggling separate trackers for "the build" and "the support contract."
A Realistic Scenario: 8-Person Web Dev Agency
Picture an 8-person agency in the Pacific Northwest that builds custom marketing sites and headless commerce stores, mostly in the $40k-$120k range. Three senior engineers, two designers, one PM, one QA, one owner-operator running sales. Around six active builds at any time and a roster of 12 maintenance retainers.
Before: Asana for client tasks, Linear for engineering, Harvest for time, QuickBooks for invoicing, a custom Laravel portal someone built three years ago that no one wants to update, Notion for SOWs. The owner-operator spends roughly four hours every Friday assembling invoices and another two on Monday morning chasing late payments. Change orders are tracked in an email folder labeled "scope."
After 90 days on AgencyPro: Asana is gone. Harvest is gone. The Laravel portal is gone. Invoices fire on milestone completion; the Friday invoicing block drops from four hours to about 30 minutes of review-and-send. Change orders live in the project as approved line items, and a quarterly review uncovers around $7,400 in previously unbilled mid-build work across six projects — work that absolutely happened but had been absorbed silently because no one wanted to send the awkward email.
Where it actually moves the business: Phase-level reporting reveals that backend hours on the last four headless commerce builds have averaged 1.6x the original estimate. The agency raises its backend hourly rate on new proposals by 20% and adjusts its scoping template. The next three signed builds land at a gross margin 8-12 points higher than the trailing average, which is the kind of structural win a $39-$79/month tool subscription does not show up as a line item against.
Resources for Web Development Agencies
Guides, templates and tools to help you run a more profitable web development agency.
Software Development Invoice Template
Professional invoice template designed for development services.
How to Prevent Scope Creep
Master scope management and protect your development project margins.
Project Profitability Calculator
Plug in actual hours and rates to see real margin on your last build.
Software Development Agencies
Sprint-based workflows for custom software development agencies.