5 Best Accounting Software for E-commerce 2025

5 Best Accounting Software for E-commerce 2025

5 Best Accounting Software for E-commerce 2025

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In selecting the right accounting software program for e-commerce companies, I like to recommend one that may sync transactions between the e-commerce platform and accounting software program, observe multi-channel gross sales, reconcile funds, deal with gross sales tax, and automate COGS and returns for correct reporting. With that in thoughts, listed below are the software program that made it to my record:

Fast comparability of the very best accounting software program for e-commerce

Month-to-month value
My general ranking (out of 5)
Accounting options ranking (out of 5)
E-commerce options ranking (out of 5)
QuickBooks On-line
$35 to $235
4.4
4.7
4.0
Xero
$20 to $80
4.2
4.7
3.6
Zoho Books
$0 to $240
4.1
4.8
3.3
Sage Intacct
Customized
3.9
5.0
3.2
Wave
$0 or $16
3.3
3.3
1.6
Score: 5 (Glorious); 4 (Very Good); 3 (Good); 2 (Honest); 1 (Poor). For an in depth clarification, examine my methodology under.

QuickBooks On-line: Finest general

Quickbooks Online Logo.
picture quickbooks on line

My ranking: 4.4 out of 5

QuickBooks On-line leads my roundup of the very best e-commerce accounting software program, primarily as a result of it affords direct integrations with Shopify and BigCommerce. Whereas platforms like Amazon, eBay, and Squarespace lack native QuickBooks connections, they sync seamlessly by third-party connectors like A2X, Zapier, and Webgility — all of which combine effectively with QuickBooks On-line.

Past its highly effective options, QuickBooks is broadly used throughout the US. This makes it a super selection in the event you’re trying to outsource bookkeeping to unbiased CPAs or companies specializing in e-commerce accounting.

Pricing

  • Easy Begin: $35 monthly for one seat
  • Necessities: $65 monthly for 2 customers
  • Plus: $99 monthly for 5 seats
  • Superior: $235 monthly for 25 customers

You possibly can strive QuickBooks On-line free for 30 days or get a 50% low cost for 3 months in the event you join immediately.

My analysis

QuickBooks On-line earns excessive marks for each accounting and e-commerce performance. Its energy in accounting is anticipated, given its versatility, however what stands out is its e-commerce adaptability. Whereas not an e-commerce platform itself, QuickBooks On-line integrates instantly and through third-party apps with main e-commerce platforms. The built-in Mailchimp integration inside Intuit additionally makes deserted cart e mail automation seamless.

Furthermore, it did effectively in ecommerce options as a result of its robust integrations and automation however misplaced factors for missing built-in deserted cart monitoring and superior market reporting. Whereas it syncs with Shopify, Amazon, and eBay, multi-channel sellers might have third-party apps like A2X for detailed income attribution and reconciliation. Regardless of this, it stays a best choice for small or midsize companies.

The primary disadvantage of QuickBooks On-line is scalability, because it limits the variety of seats to a most of 25. In case you want extra customers, Xero could be the higher possibility. However in the event you want extra seats and have outgrown QuickBooks, I extremely suggest Sage Intacct.

Learn our QuickBooks On-line evaluation

Professionals and cons

Professionals Cons
  • Syncs seamlessly with Shopify and BigCommerce
  • Tracks COGS precisely with stock administration integrations
  • Reconciles funds from Stripe, PayPal, and different processors with minimal guide work
  • Offers detailed monetary experiences with gross sales channel breakdowns
  • Lacks native deserted cart income monitoring and attribution
  • Requires third-party apps for superior e-commerce analytics
  • Prices further for multicurrency transactions
  • Struggles with excessive transaction volumes, resulting in occasional slowdowns

Xero: Finest for rising firms with multicurrency wants

Xero Logo.
picture xero

My ranking: 4.2 out of 5

Xero is my choose for rising firms as a result of it supplies limitless seats in all plans. On prime of that, it affords excellent options in multicurrency transactions, making it an important choose for e-commerce companies with worldwide transactions.

It additionally integrates with Shopify, Amazon, WooCommerce, BigCommerce, and extra through third-party apps like A2X, Webgility, and Synder. These integrations automate gross sales knowledge syncing, tax calculations, and COGS monitoring. Its financial institution feeds and automated reconciliation streamline fee processing from Stripe, PayPal, and different gateways, lowering guide work.

Pricing

  • Early: $20 monthly (restricted to twenty invoices and 5 payments)
  • Rising: $47 monthly
  • Established: $80 monthly

Get 90% off for 3 months once you join, or strive a plan for 30 days and pay the common price after the trial.

My analysis

Xero goes head-to-head with QuickBooks On-line however stands out for scalability and world e-commerce assist. In contrast to QuickBooks, it permits limitless customers, making it excellent for rising companies needing entry for accountants, finance groups, and e-commerce managers.

One other key benefit is its multicurrency assist. It routinely converts transactions in over 160 currencies with real-time trade charges, which is crucial for worldwide gross sales on platforms like Amazon, Shopify, and eBay.

Nevertheless, Xero didn’t rating as excessive in e-commerce options as a result of its integration choices and reporting capabilities aren’t as polished. The platform’s editor lacks flexibility, making it irritating to customise experiences or streamline workflows for e-commerce companies. Moreover, Xero is much less fashionable within the US, the place QuickBooks On-line dominates the market. Many US CPAs and bookkeepers are QuickBooks ProAdvisors, making QuickBooks On-line excellent for companies desirous to outsource their bookkeeping.

Learn our evaluation of Xero

Professionals and cons

Professionals Cons
  • Syncs with Shopify, Amazon, eBay, and different platforms through third-party apps
  • Helps multicurrency transactions and automated trade price updates
  • Automates gross sales tax monitoring and integrates with Avalara for compliance
  • Offers customizable monetary experiences with multi-channel monitoring
  • Limits automation for high-volume e-commerce companies
  • Prices further for multicurrency performance
  • Lacks native integration for deserted cart income monitoring

Zoho Books: Finest for automation and customization

Zoho Books Logo.
picture zoho books

My ranking: 4.1 out of 5

Zoho Books is tightly built-in throughout the Zoho ecosystem, making it an important selection for e-commerce companies utilizing Zoho Commerce, Zoho CRM, or Zoho Stock. Its built-in automation reduces guide work and seamless knowledge syncing retains financials up to date throughout platforms.

With a number of integrations throughout the Zoho atmosphere, it provides companies centralized management over gross sales, accounting, and stock. Options like automated invoicing, tax monitoring, and order administration simplify e-commerce operations. Although it lacks direct Amazon or eBay integrations, instruments like Zapier and Zoho Stream assist bridge the hole, making it a versatile and automation-friendly possibility for e-commerce sellers.

Pricing

  • Free: For one consumer solely
  • Customary: $15 monthly for 3 seats
  • Skilled: $40 monthly for 5 customers
  • Premium: $60 monthly for 10 seats
  • Elite: $120 monthly for 10 customers
  • Final: $240 monthly for 15 seats

Extra seats price $11 per consumer, monthly.

My analysis

Zoho Books earns a excessive mark in accounting options — no surprises there. Nevertheless, its e-commerce options took successful as a result of lack of direct integrations with main e-commerce platforms. Whereas Zoho Books integrates with Zoho Commerce, that isn’t a major platform in my analysis, although I nonetheless awarded further factors for it.

What actually units Zoho Books aside, although, is its excellent buyer assist, which outperformed many rivals. You possibly can contact the crew through telephone, e mail, and stay chat, whereas an intensive data base is offered for fast solutions.

Although Zoho Books affords integrations with different Zoho apps, there’s quite a lot of competitors out there which will steer you away from Zoho’s different choices. When you have no plans to remain throughout the Zoho app ecosystem, I like to recommend going with Xero as a result of it supplies extra flexibility with third-party integrations, stronger multi-currency assist, and limitless consumer entry.

Learn our Zoho Books evaluation

Professionals and cons

Professionals Cons
  • Integrates natively with Zoho Commerce and helps third-party e-commerce apps
  • Automates COGS monitoring and stock changes
  • Tracks multi-channel gross sales and income attribution
  • Helps customizable monetary reporting and multicurrency transactions
  • Contains built-in gross sales tax administration with compliance monitoring
  • Requires third-party apps for Amazon, eBay, and Walmart integration
  • Lacks direct integration with deserted cart monitoring instruments
  • Limits scalability for big companies with advanced accounting wants
  • Doesn’t supply robust multi-entity administration like enterprise-level options
  • Has a smaller community of licensed bookkeepers within the US than rivals

Sage Intacct: Finest for multi-entity firms

Sage Intacct Logo.
picture sage

My ranking: 3.9 out of 5

Sage Intacct is a stable choose if your organization manages a number of organizations. Due to its built-in consolidation options, Sage Intacct makes accounting for intercompany transactions straightforward. It automates eliminations, multi-entity reporting, and forex conversions, lowering the guide work usually required for consolidated financials.

Past its energy in multi-entity administration, Sage Intacct additionally excels in superior monetary reporting, providing customizable dashboards and deep analytics for e-commerce companies dealing with excessive transaction volumes. Its automation capabilities lengthen to stock monitoring, order administration, and income recognition, making it well-suited for large-scale e-commerce operations.

Pricing

Contact Sage for a customized quote.

My analysis

General, Sage Intacct carried out effectively. It’s the one supplier that aced my evaluation of accounting options, excelling in income administration and multi-entity accounting. That makes it a powerful selection for e-commerce companies needing superior monetary instruments.

It scored decrease in e-commerce options as a result of its lack of direct integrations with Shopify, Amazon, and eBay, counting on third-party connectors that add complexity and price. It additionally lacks native deserted cart monitoring and multi-channel income attribution, requiring extra software program to fill these gaps. Whereas its automation and reporting are robust, the absence of built-in e-commerce instruments makes it much less excellent for sellers needing seamless platform connectivity.

Furthermore, it solely scored solely above common in ease of use, primarily as a result of restricted bookkeeping assist within the US. Whereas Sage Advisors can be found, the community isn’t as widespread as QuickBooks ProAdvisors, which nonetheless dominates the market.

Learn our evaluation of Sage

Professionals and cons

Professionals Cons
  • Manages multi-entity accounting with real-time consolidated financials
  • Tracks e-commerce income attribution with multi-touch modeling
  • Automates superior stock and COGS monitoring
  • Helps multicurrency, tax compliance, and customized monetary reporting
  • Handles excessive transaction volumes effectively
  • Requires professional setup as a result of advanced configuration
  • Prices considerably greater costs than different e-commerce accounting options
  • Limits direct e-commerce integrations, counting on third-party connectors
  • Requires extra modules for full automation of returns and refunds

Wave: Finest for brand new e-commerce sellers

Wave Logo.
picture wave

My ranking: 3.3 out of 5

In case you’re simply beginning your e-commerce retailer and have fewer gross sales, Wave is the right easy accounting resolution for monitoring e-commerce earnings and bills. Because it’s free, it’s excellent for companies wanting to maintain prices low whereas managing fundamental bookkeeping. In case you’re an e-commerce vendor who sells part-time and has no plan of scaling up, selecting Wave is an economical possibility.

Pricing

  • Starter: Free for one consumer
  • Professional: $16 for limitless customers

My analysis

Wave has a “glass ceiling” when it comes to capabilities and long-term use. It affords easy accounting options that work for small e-commerce shops or informal sellers. Nevertheless, it lacks built-in COGS monitoring, which may be difficult for companies dealing with excessive gross sales volumes. For smaller shops, monitoring COGS manually in a spreadsheet should still be manageable.

The platform additionally has restricted e-commerce integrations, so don’t count on automated stock syncing, multi-channel income monitoring, or superior gross sales tax automation. If you wish to keep free however have the choice to improve and scale, I like to recommend selecting Zoho Books. Its free tier is nice for informal e-commerce.

Learn our Wave evaluation

Professionals and cons

Professionals Cons
  • Offers free accounting software program for small e-commerce companies
  • Tracks earnings and bills with easy financial institution reconciliation
  • Affords fundamental invoicing and fee processing
  • Helps automated tax calculations for US gross sales tax
  • Integrates with Zapier for expanded e-commerce connections
  • Lacks direct integration with Shopify, Amazon, or main e-commerce platforms
  • Requires guide transaction imports for gross sales channel monitoring
  • Doesn’t assist COGS automation or stock administration
  • Lacks multi-entity assist and superior monetary reporting
  • Affords restricted bookkeeping assist with no devoted advisor community

How I evaluated the very best e-commerce accounting software program

I used a rubric to judge the 5 finest accounting software program for e-commerce companies.

Pricing (10% of general rating)

This breaks down the true price and worth of accounting software program, guaranteeing you get worth for cash. The bottom subscription and extra consumer prices are measured in opposition to affordability, with greater scores awarded to a program that retains pricing affordable. Moreover, the features-to-cost ratio reveals whether or not a instrument’s price ticket is justified by its capabilities, rewarding those who ship robust performance with out inflating prices.

Accounting options (40% of general rating)

My evaluation focuses on core accounting capabilities, together with transaction administration, monetary reporting, and automation. I evaluation how effectively the software program helps e-commerce companies, notably in areas like tax compliance, stock monitoring, and multi-entity accounting. Usability, customization, and scalability are additionally key elements, guaranteeing the instrument meets the wants of rising companies.

E-commerce options (20% of general rating)

This focuses on platform integrations, fee reconciliation, and transaction automation to make sure seamless monetary monitoring. I look at how effectively the software program handles deserted cart monitoring, income attribution, and returns administration, serving to you optimize gross sales and profitability. Moreover, I contemplate multi-channel gross sales assist and reporting accuracy, guaranteeing you possibly can observe efficiency throughout totally different platforms and advertising and marketing sources.

Ease of use and assist (20% of general rating)

I consider usability, assist, and accessibility, guaranteeing you possibly can effectively handle accounting processes. I additionally evaluation bookkeeping assist, dashboard navigation, and studying curve, specializing in how intuitive the software program is and the way simply you possibly can arrange and combine e-commerce platforms. Moreover, I look at buyer assist high quality, together with response instances, out there sources, and the accessibility of licensed bookkeeping professionals.

Person evaluations (10% of general rating)

I additionally take consumer suggestions from G2 and Capterra into consideration. I exploit the weighted common scores of these two evaluation websites as a foundation for the consumer evaluation rating.

Rankings

I gave the next base rankings to attain software program.

  • Glorious (5): The function is totally developed, extremely automated, and seamless. It requires little or no guide effort, integrates easily with different techniques, and contains superior capabilities that enhance effectivity or present further worth past fundamental expectations.
  • Very Good (4): The function is well-designed and efficient however has minor limitations which will require occasional professional changes. It really works reliably and contains most anticipated performance however could lack some refinements or superior settings.
  • Good (3): The function meets fundamental necessities however has noticeable gaps that might influence usability. It features as anticipated however requires some guide work or professional enter to function effectively. It’s usable however not the very best in its class.
  • Honest (2): The function exists however is underdeveloped or lacks key features. It could be troublesome to make use of, require frequent workarounds, or rely closely on professional tweaks to carry out important duties. It’s useful however irritating or incomplete.
  • Poor (1): The function is barely usable, unreliable, or doesn’t carry out as supposed. It could have vital limitations, have frequent errors, or lack key integrations, making it impractical for real-world use.
  • N/A (0): The function is totally lacking from the software program, that means customers should depend on third-party options, workarounds, or guide processes to compensate for its absence.

Along with the bottom ranking, I utilized professional changes, including 0.1 to 0.5 factors primarily based on key strengths or enhancements that enhance performance. These changes fine-tune the scores to replicate usability, effectivity, and concord if mixed with different options.

Ceaselessly requested questions (FAQs)

Is QuickBooks good for an e-commerce enterprise?

Sure, it’s. It integrates with Shopify, Amazon, eBay, and different platforms, automates gross sales tax monitoring, and simplifies COGS monitoring, multi-channel income reporting, and fee reconciliation. Its third-party app market additionally expands performance for stock administration and superior analytics.

Which accounting software program is finest for Shopify?

QuickBooks On-line, Xero, and Zoho Books are prime decisions for Shopify, relying on enterprise dimension and desires. QuickBooks On-line affords direct integration, automated gross sales monitoring, and robust monetary reporting. In the meantime, Xero is perfect for multicurrency assist and automation, whereas Zoho Books is good for companies already utilizing Zoho’s ecosystem and needing affordability with automation.

What’s the finest accounting software program for Amazon sellers?

QuickBooks On-line, Xero, and Sage Intacct stand out. QuickBooks On-line integrates with Amazon Vendor Central through apps like A2X, making gross sales reconciliation and COGS monitoring seamless, whereas Xero is a powerful various with multicurrency assist and automatic financial institution feeds. Sage Intacct is good for high-volume Amazon sellers needing superior stock administration and multi-entity accounting.

author avatar
roosho Senior Engineer (Technical Services)
I am Rakib Raihan RooSho, Jack of all IT Trades. You got it right. Good for nothing. I try a lot of things and fail more than that. That's how I learn. Whenever I succeed, I note that in my cookbook. Eventually, that became my blog. 
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