They are not really competitors
The question is usually framed as a choice, but ShipBob and Amazon FBA solve different halves of the same problem. FBA fulfils Amazon orders with Prime eligibility attached. ShipBob fulfils orders from your own store and other channels from a distributed network. Sellers who treat it as either-or normally end up overpaying on one side.
Where FBA wins
For orders placed on Amazon, FBA is hard to beat. The per-unit fulfillment fee is competitive, the Prime badge lifts conversion measurably, and Amazon handles customer service and returns intake. If most of your revenue is Amazon revenue, moving that volume to a third-party 3PL usually costs you more in lost conversion than you save in fees.
Where ShipBob wins
For your own Shopify store, for eBay, for Walmart and for any non-Amazon channel, FBA Multi-Channel Fulfillment is expensive and slower than it should be. A 3PL like ShipBob is normally the cheaper way to serve those orders, and you keep control of packaging and the unboxing experience, which matters for brands.
The cost nobody models properly: storage
Amazon storage fees plus the utilization surcharge plus long-term storage fees are what actually erode margin, and they punish exactly the behaviour that prevents stockouts, which is holding cover. The fix is not choosing ShipBob over FBA. It is holding your buffer somewhere cheaper and sending Amazon only what it will sell in the next few weeks.
What most sellers settle on
A buffer of inventory held outside Amazon at low storage cost, drip-fed into FBA so Amazon orders stay Prime eligible and surcharges stay near zero, with DTC and other marketplace orders shipped from the same pool. That is the arrangement we run for sellers from our owned Austin floor, and it is why the comparison usually resolves to both rather than either.