ShipBob’s Shopify app is actually pretty good. Clean interface, decent inventory sync, reliable order routing. For a single 3PL setup with under 100 SKUs, it’s honestly one of the better integrations out there.

But here’s the thing nobody talks about: it falls apart when you scale.

The moment you add Amazon FBA to the mix, launch 500+ SKUs, or need to split inventory between multiple fulfillment centers, ShipBob’s “simple” approach becomes your biggest headache.

When “Simple” Becomes Complicated

The Single 3PL Trap

ShipBob’s app assumes you’re all-in on ShipBob. Their dashboard shows:

Available: 1,247 units
Allocated: 23 units
Awaiting: 156 units

But what if you also have:

400 units at Amazon FBA
200 units in your own warehouse
150 units at another 3PL for international shipping

ShipBob’s app can’t see any of that. Your Shopify inventory becomes a mess of manual adjustments and constant fear of overselling.

The Multi-Location Nightmare

You’re growing. You add ShipBob’s West Coast fulfillment center to complement their East Coast location. Makes sense for shipping speed, right?

Wrong.

Now your 1,000 units of PROTEIN-VANILLA-2LB are split:

ShipBob Chicago: 600 units
ShipBob Los Angeles: 400 units
Your Shopify store: Shows 1,000 units available

Customer in Miami orders 700 units. ShipBob Chicago can only fulfill 600. The remaining 100 units ship from LA, creating a split shipment that confuses your customer and doubles your shipping costs.

ShipBob’s app doesn’t give you granular control over which location fulfills which orders.

The Real-World Breakdowns

Scenario 1: The Amazon FBA Conflict

You sell supplements. High-movers go to Amazon FBA for Prime eligibility. Everything else goes to ShipBob.

Your bestseller PROTEIN-CHOCOLATE-2LB:

Amazon FBA: 500 units
ShipBob: 300 units
Total: 800 units

Customer orders 600 units on Shopify. Where should it ship from?

ShipBob’s app doesn’t know about your Amazon inventory. You either:

Manually route to Amazon (breaking ShipBob’s automatic fulfillment)
Let ShipBob fulfill 300 units and scramble to source the remaining 300
Constantly manually adjust Shopify inventory to prevent overselling

Scenario 2: The Returns Routing Chaos

Customer returns a defective product. Where does it go?

ShipBob orders: Return to ShipBob
Amazon FBA orders: Return to Amazon
Direct orders: Return to your warehouse

But ShipBob’s app doesn’t track original fulfillment source. You’re manually managing return addresses and inventory adjustments across multiple systems.

Scenario 3: The Seasonal Inventory Shuffle

Q4 hits. You need to rebalance inventory:

Move fast-movers to Amazon FBA for Prime shipping
Keep slower SKUs at ShipBob for cost efficiency
Add a third 3PL for international fulfillment

ShipBob’s app shows everything as “available” regardless of location. You have no visibility into:

Which SKUs are where
How to rebalance efficiently
What the cost implications are

The SKU Mapping Complexity

ShipBob’s app handles basic SKU mapping well. Your BLUE-HOODIE-XL stays BLUE-HOODIE-XL in ShipBob’s system. Clean and simple.

But add multiple 3PLs and it breaks down:

Your SKU	ShipBob	Amazon FBA	3PL International
BLUE-HOODIE-XL	BLUE-HOODIE-XL	X00-ABC-1234	BH-XL-001
RED-SHIRT-M	RED-SHIRT-M	X00-DEF-5678	RS-M-002

Now you need to track:

Which 3PL has which SKU
How much inventory is where
Which orders should route to which fulfillment center

ShipBob’s app wasn’t built for this complexity.

The Inventory Allocation Problem

Here’s a scenario that happens daily:

You have 100 units of DESK-LAMP-WHITE total:

ShipBob: 60 units
Amazon FBA: 40 units

Customer orders 80 units on Shopify. ShipBob can only fulfill 60. The logical solution is to:

Ship 60 from ShipBob
Ship 20 from Amazon FBA

But ShipBob’s app can’t orchestrate this. You need to:

Manually split the order
Create a separate Amazon order
Update inventory across multiple systems
Explain to the customer why they’re getting two shipments

ShipBob’s reporting is solid for ShipBob-only data:

Units shipped per day
Top SKUs by volume
Fulfillment speed metrics

But it can’t tell you:

Total inventory across all 3PLs
Cost comparison between fulfillment options
Optimal inventory allocation for upcoming demand

You’re flying blind on the strategic decisions that impact your bottom line.

The Hidden Costs

Time Cost:

Jennifer runs a home goods brand with 800 SKUs across ShipBob, Amazon FBA, and her own warehouse
She spends 12 hours/week manually managing inventory allocation and preventing overselling
That’s 624 hours/year = $31,200 in labor costs

Opportunity Cost:

David’s electronics company missed $67,000 in sales during Black Friday because ShipBob showed “out of stock” while Amazon FBA had 300+ units available

Customer Experience Cost:

Michelle’s fashion brand had 127 split shipments in November, leading to 34 customer complaints and 12 refund requests

What You Actually Need

1. Unified Inventory Visibility

See total available inventory across ShipBob, Amazon FBA, and other 3PLs from one dashboard.

2. Intelligent Order Routing

Automatically route orders to the optimal fulfillment center based on:

Inventory availability
Shipping cost and speed
Customer location

3. Multi-3PL Inventory Sync

Keep Shopify inventory accurate across all fulfillment channels, not just ShipBob.

4. Exception Handling

Get alerts when:

Orders can’t be fulfilled from the assigned 3PL
Inventory needs rebalancing
SKUs are missing from certain locations

How SKU Wrangler Bridges the Gap

We built SKU Wrangler because ShipBob’s app is great at what it does, but it’s not built for complex multi-3PL operations.

Unified Inventory Dashboard: See inventory across ShipBob, Amazon FBA, and other 3PLs in one place.

Smart Order Routing: Automatically route orders to the best fulfillment option based on inventory, cost, and shipping speed.

Multi-3PL Sync: Keep Shopify inventory accurate across all channels, preventing overselling and stockouts.

Allocation Optimization: Get recommendations on how to distribute inventory across 3PLs for maximum efficiency.

The Bottom Line

ShipBob’s Shopify app is solid for single-3PL operations. But if you’re scaling with multiple fulfillment partners, thousands of SKUs, or complex inventory needs, you need more than what any single 3PL can provide.

The goal isn’t to replace ShipBob’s app - it’s to layer intelligence on top of it. To turn your multi-3PL complexity into a competitive advantage instead of a daily headache.

Ready to scale beyond single-3PL limitations? Get early access to SKU Wrangler and see how we orchestrate complex fulfillment operations.

ShipBob + Shopify Works Great... Until It Doesn't