Freight invoices. The quiet line item that can wreck your e-commerce books.

Freight invoices are rarely exciting. No one starts an e-commerce brand dreaming about reconciling DHL, FedEx, local couriers, 3PL handling fees, fuel levies, port charges, or customs clearance lines.

But here’s the thing.
For product businesses, freight invoices quietly decide whether your numbers make sense or slowly drift off course.

If you’re a bookkeeper or a small e-commerce business owner, you’ve probably felt it. That nagging feeling when COGS looks a bit odd. Or GST doesn’t quite line up. Or freight expenses balloon month to month and nobody can clearly explain why.

Freight invoices are messy by nature. And most accounting tools were never really designed for how freight actually works.

Let’s talk about why freight invoices matter so much in e-commerce, why they’re such a pain to process, and how Pulsify handles multi-account, multi-tax freight invoices without the usual gymnastics.

Why freight invoices matter more than people think

On paper, freight feels like “just another expense.”
In reality, it touches almost everything.

For e-commerce businesses, freight costs directly affect:

• Landed cost calculations

• Gross margin accuracy

• Inventory valuation

• GST and tax reporting

• Supplier and carrier reconciliation

• Cash flow forecasting

Get freight wrong and your P&L lies to you. Not dramatically. Quietly. Over time.

And because freight often sits outside “nice clean” supplier bills, it’s where errors hide the longest.

You know what usually happens.
Freight gets dumped into a single account. Or coded inconsistently depending on who processed the invoice that day. Or split roughly “based on last time” because no one wants to manually review 40 line items again.

That works. Until it doesn’t.

The reality of freight invoices in e-commerce

Let’s be honest. Freight invoices are chaos compared to a standard supplier bill.

A single freight invoice can include:

• Line-haul charges

• Fuel surcharges

• Remote delivery fees

• Port and terminal handling

• Customs clearance

• Insurance

• Duties and taxes

• Local delivery legs

• Recharges from 3PLs

Each of those lines can need a different account. Sometimes different tax treatment too.

And unlike a neat SaaS invoice, freight invoices love variation. Layouts change. Line descriptions are inconsistent. Carriers rename fees. Tax rules shift depending on origin, destination, and service type.

If you’re working in e-commerce bookkeeping, you already know this pain intimately.

Multi-account coding. Where things usually fall apart.

Freight invoices almost never belong in one account.

A single invoice might need to be split across:

• Freight in or freight out

• COGS vs operating expenses

• Duties and customs accounts

• Fuel surcharge accounts

• Clearing or suspense accounts

Most invoice automation tools stop at extraction. They grab totals, dates, supplier names, and maybe GST.

Then they hand the mess to you.

That’s fine for simple bills. It’s brutal for freight.

So bookkeepers end up:

• Manually splitting invoices line by line

• Copying last month’s coding and hoping it still applies

• Letting junior staff guess and fixing it later

• Or worse, dumping it all into one account just to keep things moving

Multiply that by dozens or hundreds of freight invoices per month and suddenly “automation” hasn’t really saved time at all.

Multi-tax line items. The quiet GST headache.

Freight invoices don’t just test your patience. They test your tax logic.

A single invoice might include:

• GST-free international freight

• Taxable domestic legs

• Import duties with no GST

• Fees that attract GST even if the core freight doesn’t

OCR alone can’t figure that out. And blanket tax rules break down fast.

This is where bookkeepers start second-guessing themselves.
“Was this GST-free last time?”
“Does this line get BAS excluded?”
“Why is this carrier charging GST on only part of the invoice?”

Miss it once and the BAS still lodges. Miss it consistently and the cleanup later is painful.

Why most invoice automation tools struggle with freight

Tools like Dext and Hubdoc do a solid job at what they were built for. Capturing documents. Extracting data. Getting bills into Xero or MYOB quickly.

But freight invoices sit outside their comfort zone.

They’re not uniform.
They’re not predictable.
And they’re not single-account, single-tax bills.

Most tools treat invoices as flat objects. One supplier. One total. One tax logic.

Freight invoices are layered. Context matters.

That’s the gap.

Where Pulsify approaches freight differently

Pulsify was built with physical-goods businesses in mind. E-commerce, wholesale, manufacturing, logistics heavy operations.

So freight wasn’t an edge case. It was a core use case.

Instead of asking “How do we extract this invoice?”, Pulsify asks “How does this invoice actually behave in the ledger?”

That mindset changes everything.

Line-item level intelligence, not just OCR

Pulsify doesn’t stop at pulling text from a PDF.

It understands freight invoices at the line-item level. Each charge is treated as its own decision point, not just part of a lump sum.

That means:

• Individual line items can be mapped to different accounts

• Different tax rules can apply per line

• Repeating charges learn from past coding

• Exceptions are flagged instead of silently passed through

So when a carrier invoice arrives with fuel surcharge, line-haul, and customs clearance all bundled together, Pulsify doesn’t shrug and guess.

It separates them. Properly.

Multiple accounts without manual splitting

This is where bookkeepers usually lose the most time.

In Pulsify, multi-account freight invoices don’t require manual line splitting inside Xero or MYOB.

You can set logic like:

• Line descriptions containing “fuel” map to Fuel Surcharge

• “Customs” or “clearance” map to Duties and Fees

• International freight maps to Freight In

• Domestic delivery maps to Freight Out

Once that logic exists, Pulsify applies it consistently.

And when something new appears? It doesn’t pretend to know. It flags it for review.

That balance matters. Automation where it’s confident. Human review where it’s not.

Handling mixed tax freight invoices without stress

Tax on freight is nuanced. Pulsify doesn’t force one GST rule across an entire invoice.

Each line item carries its own tax treatment.

So an invoice with:

• GST-free international freight

• Taxable domestic legs

• GST-excluded duties

Can be processed correctly in one pass.

Bookkeepers don’t have to override half the invoice or manually adjust after sync. The logic lives with the line item, where it belongs.

Why this matters for scaling e-commerce businesses

At low volumes, messy freight coding is annoying but survivable.

At scale, it’s dangerous.

As invoice volume increases:

• Manual review becomes a bottleneck

• Junior staff make more assumptions

• Consistency breaks down across entities

• Margin reporting becomes unreliable

Freight is one of the fastest growing cost lines for e-commerce brands. Especially those dealing with international suppliers, multiple warehouses, and hybrid fulfillment models.

If freight invoices aren’t handled cleanly, every downstream report is compromised.

And founders notice. Even if they can’t quite put their finger on why the numbers feel off.

Bookkeepers feel this pain first

Bookkeepers are usually the first to see the cracks.

They’re the ones:

• Reconciling strange variances

• Answering client questions about margins

• Fixing BAS issues caused by mis-coded freight

• Cleaning up month-end journals

Freight invoices quietly eat time. And mental energy.

Tools that claim to “automate invoices” but ignore freight complexity just move the work, they don’t remove it.

Freight is where bookkeeping AI actually needs to think

This is where bookkeeping AI earns its keep.

Not by replacing judgment. But by reducing repetition.

Freight invoices repeat patterns. Same carriers. Similar charges. Familiar tax treatments. Until something changes.

Pulsify learns those patterns and applies them consistently. When a charge breaks the pattern, it asks for help.

That’s what good accounting AI should do.

The bigger picture. Cleaner freight, clearer decisions.

When freight invoices are handled properly:

• Landed costs become reliable

• Margins reflect reality

• Inventory valuation improves

• Tax risk drops

• Month-end becomes calmer

And suddenly freight stops being a source of quiet dread.

It becomes just another process that works.

Final thought

Freight invoices aren’t glamorous. They don’t get talked about in flashy accounting demos.

But for e-commerce businesses, they matter more than most people realise.

If you’re a bookkeeper juggling freight-heavy clients, or a product business wondering why your numbers never quite line up, freight is a good place to look.

And if your current tools treat freight like a flat PDF with a total at the bottom, you’re doing too much thinking manually.

Pulsify was built for this exact mess.
Multiple accounts. Mixed tax. Real-world freight invoices.

Because the boring stuff is where accuracy actually lives.