Best Accounting Software for Logistics Businesses

Why logistics businesses need proper accounting software

Think of your operations team. They are handling FOB, EXW, DAP, air freight, sea freight, LCL, FCL, cross-dock, customs, last mile, agents, carriers, pick up, and delivery. On the other side, finance is trying to make sense of this avalanche of charges, rates, and documents.

Here is where the real mess happens.

1. You deal with crazy shipment volume

Even a small forwarding team handles dozens of shipments a week. Each shipment has its own stack of charges. One missed fuel surcharge or handling fee might not hurt, but multiply that mistake across the entire month and suddenly you realise you have been working hard for money you never billed.

2. There are too many parties involved

Customer, carrier, CFS, agent, customs broker, warehouse, transporter, last mile partner.
Everyone wants their piece. Everyone sends invoices. Everyone expects quick responses. Accounting software must track all these moving parts accurately.

3. You need profit per job, not per month

A shipment that looks good in revenue might be a complete loss after you factor in agent fees, airline surcharges, delivery charges, customs handling, and detention.

Generic accounting tools cannot show job-wise profitability. They only show the monthly P and L. That is useless for real decision-making.

4. Multiple currencies are in your everyday life

USD, AED, SGD, EUR, INR.
Buy in one currency, sell in another, settle with an agent in a third.
If your accounting system cannot calculate gains and losses correctly, you will never know your true margins.

5. Cash flow improves only when invoicing is fast

In logistics, delays in billing kill cash flow. If your accounts team waits for operation sheets, WhatsApp updates, attachments, PODs, HAWB, MAWB, BL copies, the invoice goes out late. Then the payment is delayed. Then you chase. Then operations get frustrated. It becomes a cycle.

A good accounting system stops that cycle.

6. Compliance and documentation are non-negotiable

E invoicing, customs documentation, GST or VAT filing, audit trail, proof of movement.
You cannot afford mistakes here.

Why generic accounting software does not work for logistics

I know many companies that run on Tally, QuickBooks, Zoho Books, or Excel. And they say it works. It works until it doesn’t.

Here are the most common problems.

1. No shipment-wise costing

You cannot see which job made money and which job lost money. You only see totals. That is like driving while looking at the mirror instead of the road.

2. Operations and accounts never match

Operations enter charges in one place.
Finance enters them again.
Something always gets missed or doubled.
This is the main reason for revenue leakage.

3. Missed billing

Fuel surcharge, BAF, documentation, handling, and CFS fees.
Most generic tools do not remind you to bill them.
One forgotten charge is pure loss.

4. No carrier and agent reconciliation

Airlines, shipping lines, trucking vendors, CFS, agents.
You need to compare buy and sell rates without manual effort.
Generic tools cannot do that.

5. Slow invoicing

Because nothing is connected, accounts wait for operations to send job sheets.
This slows down billing and kills cash flow.

6. No multi-branch or multi-country consolidation

Most logistics firms grow by adding branches or partners in new cities.
Generic software struggles with this.

7. Heavy Excel dependency

The moment you see multiple Excel files inside a logistics office, you know the accounting system is not doing its job.

Top Accounting Tools for Logistics Companies by Business Size

If you have worked in logistics even for a short time, you already know—this industry doesn't forgive mistakes. One job moves through multiple hands, currencies, charges, and documents. Yet many logistics companies still run accounting on tools that were never designed for this complexity.

This guide breaks down why logistics needs specialised accounting software and gives you the best tools based on business size.

1. For Small Logistics Businesses

a) Xero (with logistics integrations)

Perfect for:
Small trucking companies, courier operators, and domestic logistics teams.

Why it works:

• Clean, simple accounting
  
  

• Integrates with many logistics plugins
  
  

• Easy for small teams to adopt
  
  

b) QuickBooks

Best for:
Very small transporters or freight agents who need basic accounting.

What it does well:

• Easy invoicing
  
  

• Simple books
  
  

• Affordable pricing

Not recommended for:
Multi-branch, international freight, or complex shipments.

2. For Medium Logistics Businesses

a) CargoEZ

Best for:
Small to mid-sized freight forwarders who need logistics-specific accounting without complexity.

What teams like:

• Job-wise costing is built into shipment workflows
  
  

• Multi-currency and agent/carrier settlements
  
  

• Faster invoicing with auto-attached shipment documents
  
  

• Branch-level and consolidated visibility

Why it fits this segment:
It balances logistics-first features with simplicity, ideal for companies growing beyond spreadsheets or generic tools.

b) LogiSys

Best for:
Growing freight companies that need operations and accounting to be connected.

Where it helps:

• Sync between operations and finance
  
  

• Job profitability calculations
  
  

• Handles moderate multi-branch setups

3. For Large Logistics Businesses

a) SAP Business One (logistics add-ons)

Great for teams that need a powerful ERP backbone. Takes effort to set up, but once ready, it handles finance + logistics seamlessly.

b) NetSuite ERP

Ideal for:
Enterprises with complex supply chain structures.

Key benefits:

• Strong analytics
  
  

• Works across countries and departments
  
  

• Supports large-volume financial workflows

How to choose the right one

Ask yourself:

Are you tracking profitability per job?

Do you use multiple currencies?
Do you handle both air and sea?
Do you depend heavily on agents?
Do you struggle with missed billing
Is your invoicing slow?
Do you still rely on Excel job sheets?

If yes, you need logistics accounting software. Not a generic one.

Final thought

Logistics accounting is not like normal accounting. Our industry deals with complex shipments, multiple parties, fluctuating charges, and multi-currency workflows. A generic accounting tool can only take you so far before errors, delays, and missed charges start affecting profits.

A logistics-specific system gives you cleaner data, faster invoicing, better control over margins, and real visibility into whether each shipment is actually making money. Tools like CargoEZ make this shift easier by giving smaller and mid-sized logistics teams the accounting structure they need without complicating daily operations.

Frequently Asked Questions (FAQs)