Amazon vs Shopify Fulfillment: FBA, 3PL, or Both?

FBA: the Amazon default

Fulfillment by Amazon handles storage, picking, packing, and shipping for Amazon orders. You ship inventory to Amazon's warehouses, and they handle everything from there.

The Prime advantage: FBA products get Prime eligibility. Over 200 million Prime members actively prefer Prime-eligible products. The Prime badge increases conversion rates by 20-50% depending on category. This single benefit makes FBA the default choice for Amazon orders.

Costs: FBA fees range from $3.22 (small standard) to $15+ (oversized). Monthly storage: $0.87/cubic foot (Jan-Sep), $2.40/cubic foot (Oct-Dec). See our complete FBA fee breakdown.

Pros: Prime badge, hands-off fulfillment, Amazon handles returns and customer service for fulfillment issues, automatic scaling during peak periods, multi-channel fulfillment option (MCF).

Cons: Storage fees add up (especially in Q4), less control over packaging and branding, commingling risks (if you use stickerless inventory), Amazon's return policy applies (very customer-friendly, sometimes too generous for sellers).

FBM: merchant-fulfilled

With Fulfillment by Merchant, you handle storage and shipping yourself — from your home, office, or warehouse. You list on Amazon but manage the entire fulfillment process.

When it makes sense: Heavy or oversized items where FBA fees are prohibitive, fragile products requiring special packaging, products with very low sales velocity (FBA storage costs exceed the benefit), or custom/made-to-order products.

The downside: No Prime badge (unless you qualify for Seller Fulfilled Prime, which has strict performance requirements). Lower conversion rates, and you're responsible for shipping speed, tracking, and customer service. FBM orders also drive most Order Defect Rate issues.

For a deeper comparison of FBA vs FBM, see our FBA vs FBM guide.

3PL: flexibility and control

A third-party logistics provider handles fulfillment outside of Amazon's ecosystem. Popular options include ShipBob, ShipMonk, Deliverr (now part of Shopify Fulfillment Network), and regional warehouses.

Pros: Custom branded packaging (your logo, inserts, tissue paper), lower costs for large items, multi-channel flexibility (fulfill Amazon FBM, Shopify, Walmart, and wholesale from one inventory pool), no Amazon storage limits or aged inventory surcharges, and you control the customer experience.

Cons: No Prime badge on Amazon orders, you manage the 3PL relationship and performance, variable quality across providers (vet carefully), and setup takes 2-4 weeks to onboard and integrate.

Costs: Typical 3PL pricing: $2-4 per pick and pack, $0.50-1.50 per item (additional items in same order), plus shipping (varies by carrier and destination). Monthly storage: $25-45 per pallet. For standard-size items shipping to US addresses, total fulfillment cost is typically $3-5 per order — often cheaper than FBA for items over 1 lb.

Amazon MCF: FBA for non-Amazon orders

Multi-Channel Fulfillment lets you use your FBA inventory to fulfill orders from other channels — Shopify, Walmart, your own website. Sounds appealing: one inventory pool for all channels.

The reality: MCF has significant drawbacks for DTC sellers:

• Amazon-branded packaging: Orders ship in Amazon boxes with Amazon tape. Your DTC customer gets an Amazon-branded package — confusing for your brand experience.
• Higher fees: MCF fees are 20-30% higher than standard FBA fees for the same items. Amazon charges a premium for non-Amazon fulfillment.
• No Prime speeds guaranteed: MCF orders don't get Prime delivery speeds. Standard MCF delivery is 3-5 business days.
• Limited branding: No custom inserts, no branded packing slips, no special packaging.

MCF can work as a temporary solution while you set up a 3PL, but it's not ideal as a permanent DTC fulfillment strategy.

Hybrid approaches

Most successful multi-channel sellers use a hybrid model: FBA for Amazon orders, 3PL for everything else. This gives you the best of both worlds:

• Amazon orders: FBA → Prime badge, high conversion, hands-off fulfillment
• Shopify/DTC orders: 3PL → custom branding, lower cost, better customer experience
• Wholesale orders: 3PL → palletized shipping, custom packaging

The tradeoff: you manage two inventory pools. This requires careful inventory synchronization to avoid overselling or understocking on either channel.

Cost comparison

For a typical 1-lb standard-size product shipping to a US address:

• FBA: $4.75 average (includes pick, pack, ship) + $0.40 monthly storage = ~$5.15 total
• 3PL (ShipBob/ShipMonk): $3.20 average (pick, pack) + $2.50 shipping = ~$5.70 total, but with custom branding
• MCF: $6.20 average (MCF premium) + Amazon-branded packaging
• FBM (self-fulfill): $2-3 labor + $3-5 shipping + your time = $5-8 total, no Prime badge

FBA wins on per-unit cost for Amazon orders (plus the Prime conversion lift). 3PL wins for DTC orders on branding and customer experience. MCF loses on both cost and branding.

Which to choose

Jarvio can analyze your specific product catalog, sales channels, and order volumes to recommend the optimal fulfillment split and estimate cost savings: