6 Best Accounting Software for Medical Spas (2025)

Running a medical spa means balancing artistry with precision. Behind every injectable, IV drip, or membership plan lies a financial system that must keep pace. So what’s the best accounting software for medical spas?.

Unlike standard small businesses, med spas juggle:

• High-volume retail sales
• Recurring memberships
• Payroll for multiple providers
• Vendor payments
• Strict healthcare compliance.

Without the right accounting software, errors pile up, tax prep becomes a nightmare, and growth decisions lack clarity. We’ve done some research so you can get set up quickly, without these hassles. Let’s dive in.

Why Specialized Accounting Software Matters for Medical Spas

A med spa is not a coffee shop or a boutique. Your revenue streams span injectables, weight loss programs, IV therapy, skincare products, and memberships. Each has different margins, tax implications, and compliance requirements. Add in controlled medication purchasing, HIPAA considerations, and commission-based payroll.The complexity multiplies.

Generic tools like Excel or even standard QuickBooks often fall short. They require manual reconciliation, don’t integrate with booking or EHR systems, and leave owners blind to true profitability by service line. The result? Wasted time, compliance risks, and missed opportunities.

This mirrors what we see in our platform comparisons, like Portrait Care vs GlossGenius, where clinics often end up patching multiple systems together. The gaps between tools cause reconciliation headaches. The worst part? They only grow as your patient volume scales.

Purpose-built platforms solve this by connecting financial data with clinical and operational workflows. That’s why Portrait Care stands out.

Core Features to Look for in Medical Spa Accounting Software

• Integrated Financial & Clinical Data: Your accounting system should sync directly with patient services, product sales, and payment processing.
• Revenue Tracking by Service Line: Not all services are equally profitable. Tracking injectables versus IV therapy or weight loss programs helps you allocate resources wisely.
• Automated Payroll & Expense Management: Commission splits, bonuses, and recurring expenses can get messy fast. Look for software that automates payroll and expense tracking.
• Inventory & COGS Visibility: Supplies are one of your largest cost centers. Accounting software should connect purchases, inventory, and cost of goods sold.
• Reporting & Compliance: From HIPAA-safe invoice handling to simplified tax prep, compliance is non-negotiable. Strong reporting tools also help you prepare for audits and make data-driven decisions.
• Scalability & Integrations: Whether you’re a single-location startup or a multi-location chain, your accounting system should scale with you.

The 6 Best Accounting Software for Medical Spas (2025)

1. Portrait Care

Portrait Care is more than accounting. It’s a full operating system for medical spas. It combines EHR, scheduling, payments, supply-chain purchasing, and built-in accounting tools. Trusted by 1,000+ clinics nationwide, it uniquely ties financial insights to clinical and operational data. The integrated supply savings of up to 60%+ set it apart from every other option.

Pros

• All-in-one platform: ties accounting to EHR, scheduling, payments, and inventory
• Exclusive supply chain pricing saves clinics up to 60%+
• HIPAA-compliant with built-in medical oversight
• Scales easily from single-location startups to multi-site operations
• Trusted by 1,000+ clinics nationwide

Cons

• Requires full platform adoption (not just accounting-only use)
• Might be more than needed for operators who only want a basic ledger system

Best for: Owners who want one platform to manage accounting, compliance, and growth.

If you’re comparing practice management choices, our Portrait Care vs Mindbody breakdown shows how general wellness platforms miss the financial clarity that operators need. Portrait Care remains the only solution uniting clinical, supply-chain, and accounting data in one place.

2. QuickBooks Online

A household name in small business accounting, QuickBooks offers strong bookkeeping, invoicing, and reporting. But it lacks direct integration with clinical workflows, meaning med spa owners must rely on manual reconciliation or third-party apps.

Pros

• Widely known and trusted across industries
• Strong invoicing and bookkeeping features
• Easy access to accountants familiar with QuickBooks
• Large marketplace of third-party integrations

Cons

• No native healthcare or EHR integrations
• Manual reconciliation is required for complex med spa service lines
• Extra costs for advanced features and add-ons

Best for: Practices that already use QuickBooks and don’t mind extra integrations.

3. Xero

Xero is a cloud-first platform with an intuitive interface and strong reporting dashboards. It’s flexible and user-friendly, but like QuickBooks, it isn’t built for healthcare.

Pros

• Highly intuitive and modern interface
• Strong dashboards and reporting tools
• Cloud-first accessibility with easy collaboration
• Strong support for international operations

Cons

• No direct integration with medical workflows or HIPAA safeguards
• Often requires third-party apps for payroll or advanced inventory
• Less widely adopted than QuickBooks in the US

Best for: Tech-savvy owners who want a clean interface and don’t need medical-specific features.

4. Zoho Books

Zoho Books is affordable and includes automation, invoicing, and expense tracking. It’s a good fit for smaller practices but requires separate systems for CRM and clinical management.

Pros

• Very affordable pricing tiers
• Built-in automation helps cut down admin tasks
• Part of the larger Zoho ecosystem (CRM, marketing, etc.)
• Mobile-friendly for small teams

Cons

• Lacks medical or HIPAA-focused functionality
• Separate clinical and CRM systems are required for full visibility
• Reporting is less advanced than higher-tier platforms

Best for: Lean startups looking for low-cost accounting with basic automation.

5. Sage Intacct

Sage Intacct is enterprise-level financial software with advanced reporting and scalability. It’s powerful but often too complex and costly for single-location med spas.

Pros

• Robust financial reporting and analytics
• Scales effectively for multi-location chains
• Strong compliance and audit prep features
• Industry credibility in enterprise healthcare

Cons

• Expensive setup and licensing costs
• Requires a significant learning curve and specialized training
• Overkill for single-location or startup med spas

Best for: Multi-location chains or groups with advanced accounting needs.

6. Wave

Wave is a free accounting tool with basic invoicing and expense tracking. It’s attractive for very lean startups but lacks HIPAA considerations or med spa-specific functionality.

Pros

• Free to use with no upfront cost
• Simple invoicing and expense management
• Quick setup for small teams or individuals
• Ideal for testing operations in early stages

Cons

• No HIPAA or healthcare compliance features
• Limited scalability as the business grows
• Very basic compared to professional-grade platforms

Best for: Solo operators testing the waters with minimal overhead.

Side-by-Side Comparison: Accounting Software for Medical Spas

How to Choose the Right Solution

The right accounting software depends on your size, complexity, and growth goals. Startups may prioritize affordability, but hidden labor costs from manual reconciliation add up quickly. Growing med spas need scalability, compliance, and integrated reporting to make strategic decisions.

Portrait Care uniquely combines accounting, operations, compliance, and purchasing in one intuitive platform. It’s built for ambitious operators who want to grow profitably without adding administrative burden.

Accounting software for medical spas is more than a back-office tool. The right system gives you clarity on profitability, ensures compliance, and supports smarter growth decisions. While QuickBooks, Xero, and others offer solid foundations, they lack the integration med spas need.

Portrait Care stands as the #1 choice because it connects your financials directly to your clinical and operational workflows, while delivering unmatched supply savings.

Book a demo with Portrait Care today to see how our all-in-one platform streamlines your accounting, simplifies compliance, and drives profitability, trusted by over 1,000 modern wellness clinics.

FAQ

What is the accounting software for Medspas?

Accounting software for med spas helps owners manage the unique mix of retail sales, memberships, provider payroll, and healthcare compliance. Generic tools like QuickBooks can cover basic bookkeeping, but med spas benefit most from platforms that integrate accounting with EHR, scheduling, inventory, and payment systems. The leading option for 2025 is Portrait Care, which unites financial reporting with clinical and operational data.

What is the best software for medical billing?

The best medical billing software is one that can securely process patient payments, handle insurance claims where applicable, and remain HIPAA-compliant. Many med spas rely on standalone billing tools, but Portrait Care offers built-in billing tied to patient charts, inventory, and supply chain data. This integration reduces manual reconciliation and ensures compliance while providing real-time visibility into revenue by service line.

What is the most profitable medical spa service?

Profitability varies by market, but industry benchmarks show that injectables (like Botox and fillers) consistently deliver the highest margins, often followed by IV therapy and weight loss programs. These services combine predictable demand, repeat visits, and strong cash-pay models. That’s why having accounting software that tracks profitability by service line, such as Portrait Care, is essential for making growth-focused decisions.