Best 3PLs for Shopify Stores in 2025: How to Select the Right Fulfillment Partners for Business Growth

According to 2025 statistics, Shopify has 4.82M active online stores globally, and for many of these merchants, fulfillment has become a critical hurdle as order volumes grow. If you rely on a third-party logistics for Shopify stores, they manage the warehousing, packing, and shipping tasks of your business on your behalf. By doing so, you can get time to oversee the strategic business growth and revenue gains.

However, choosing the right 3PL isn’t one-size-fits-all because every Shopify seller has unique needs in comparison to general retail. This article highlights what to look for in a Shopify-focused 3PL and reviews the top 2025 fulfillment partners with a focus on integration, support, pricing, and CPG capabilities that help you choose the right provider.

What Shopify Sellers Should Look for in a 3PL Partner?

If you want to select a 3PL company for your business, it means you are finding a partner that aligns with your store’s specific requirements. Before evaluating third-party logistics for Shopify stores, always consider:

Seamless Shopify Integration

Your 3PL should easily sync with your Shopify store to automate orders, inventory, and tracking because a direct integration or app ensures real-time updates and smooth operations.

Warehouse Network & Speed

You should evaluate the 3PL’s warehouse locations and shipping speeds because a provider with multiple fulfillment centers can offer 2-day delivery, improve reach, and boost customer satisfaction.

Transparent Pricing Structure

Fulfillment costs can be complex (storage, pick/pack fees, shipping, etc.), that’s why you should always choose a 3PL with clear and transparent pricing (rate cards, calculators, or tiered plans) to avoid hidden costs and make sure the model fits your order volume.

Experience with Your Product Type (CPG & More)

If you sell CPGs, perishables, or items needing special handling, make sure your 3PL can meet those needs. You should choose your fulfillment partner that aligns with your product type to maintain your brand’s quality.

Support & Reliability

You should select a 3PL with dependable support and accuracy because you need fast, responsive service to resolve issues before they affect your customers.

You can confidently evaluate Shopify logistics partners and find the best fit by keeping these factors in mind.

Top Shopify 3PL Fulfillment Partners in 2025

Based on your needs, here are some of the best 3PLs for Shopify in 2025. Each offers strong Shopify integration, flexible pricing, and services built to support your growth, whether you’re in CPG or another niche.

3PL Fulfillment Partner # 1: Rite Prep Fulfillment

Rite Prep Fulfillment is built specifically to serve Shopify merchants selling consumer packaged goods (CPG), so it is known as “Dedicated to CPG Fulfillment”. It offers fast and compliant shipping, and secure warehousing with an emphasis on accuracy and transparency. You get compliant, scalable fulfillment designed to protect your goods and support your growth with temperature-controlled storage and strict inventory control for CPG products. Key features of Rite Prep Fulfillment include:

• Seamless Shopify Integration: You can sync your Shopify (and other platforms) directly with Rite Prep to automate DTC and marketplace orders from Amazon, eBay, and more, hassle-free.
• Amazon FBA & FBM Prep Expertise: Rite Prep is certified to handle FBA and FBM requirements, including labeling, bundling, polybagging, and shipping inventory directly to Amazon or your end customers.
• CPG-Focused Warehousing: You’ll benefit from secure, temperature-controlled warehouses in the US, which are built for food, cosmetics, and CPG goods with strict inventory handling.
• Transparent Pricing & Support: Get straightforward, per-order pricing with no hidden fees, plus free cost estimates, fast communication, and a dedicated account manager to avoid fulfillment errors.

3PL Fulfillment Partner # 2: ShipBob

ShipBob is a leading tech-driven 3PL specializing in DTC and wholesale fulfillment for Shopify brands. It provides end-to-end warehousing, pick/pack/ship, and order management. ShipBob’s services include brand-custom packaging (inserts, gift notes, etc.) and retailer compliance support (EDI for 150+ retail partners).

As a Shopify Plus Certified App Partner, ShipBob integrates tightly with Shopify: installing the ShipBob app automatically syncs your orders and inventory in real time. Merchants see order status, inventory levels, and analytics in the ShipBob dashboard, and ShipBob can pull from multiple store channels (Shopify, Amazon, Walmart, etc.).

• Warehouse presence: ShipBob has a global fulfillment network of over 60 warehouses across North America, Europe, and Australia, which enables 2-day delivery throughout the US and abroad.
• Pricing model: ShipBob uses transparent, pay-per-use pricing. There is no startup fee or subscription, and the Shopify app is free to install. You pay per order fulfilled (with tiered rates by service level/speed) plus storage and receiving fees. All charges (in USD) appear on a monthly invoice.
• CPG brand compatibility: ShipBob actively serves many consumer-packaged goods (CPG) brands (e.g., food, supplements, personal care). It offers features like lot tracking, batch/expiry management, and eco-friendly packaging at no extra pick cost.

3PL Fulfillment Partner # 3: Red Stag Fulfillment 

Red Stag Fulfillment is a US-based 3PL built for high-value, bulky, or heavy products. They offer secure, same-day warehousing, pick/pack, and shipping with 99.98% order accuracy and full-loss protection. Their free Shopify app syncs orders in real time, which automates fulfillment without any manual steps.

• Warehouse presence: Red Stag operates 2 U.S. fulfillment centers, which are strategically positioned to reach ~96% of U.S. homes within 2 days. These facilities are equipped for heavy and bulky inventory.
• Pricing model: Red Stag offers fully transparent pay-as-you-go pricing. There are no long-term contracts or storage minimums. You pay per activity on a usage basis, and all fees are billed in USD with no hidden costs.
• CPG brand compatibility: Red Stag is ideal for CPG brands with large, fragile, or high-value goods (e.g., furniture, sporting equipment, premium supplements). Because of its error guarantee and $50 penalty payout, many CPG brands trust Red Stag with their higher-cost goods.

3PL Fulfillment Partner # 4: Shopify Fulfillment Network (SFN) 

Shopify Fulfillment Network (SFN) is Shopify’s own fulfillment service (now operated by Flexport) that lets merchants outsource warehousing and shipping through the Shopify platform. SFN provides receiving, storage, inventory management, picking, packing, shipping, and even returns handling, all managed from your Shopify admin. To use it, a merchant applies for SFN access, then designates eligible products to be stocked in SFN’s partner warehouses. When an order is placed on your Shopify store, SFN routes it to the nearest fulfillment center in its network, fulfilling it automatically. 

• Shopify integration: SFN is built into Shopify. There is a Shopify Fulfillment Network app (installed via Shopify) that connects your store to SFN. Once your products are approved, SFN fulfills orders directly from your Shopify channels, no separate login needed; everything works right within Shopify.
• Warehouse presence: SFN uses a network of U.S.-based 3PL warehouses to keep your inventory close to customers for fast, 2-day delivery. They don’t ship items over 50 lbs or larger than 50″×30″×15″.
• Pricing model: You’ll see SFN fees as one line item on your Shopify bill. You’re charged a flat per-order fee (pick, pack, ship) and monthly storage per cubic foot. For example, an order might cost ~$6.59 plus ~$2.10/month per unit for storage. Rates vary by size and weight—up to ~$124 per 50-lb item and ~$422/month for 50 units. There are no setup fees or contracts, but Shopify may require a minimum monthly order volume. Falling short can lead to higher fees. Services like returns, kitting, and audits are billed separately.
• CPG brand compatibility: SFN works best for DTC brands selling standard-sized, non-hazardous consumer goods. It doesn’t support bulky, regulated, or perishable items, or anything over 50 lbs or 40 inches.

3PL Fulfillment Partner # 3: Amazon Multi-Channel Fulfillment (MCF) 

Amazon Multi-Channel Fulfillment is Amazon’s global 3PL service that fulfills orders from any sales channel (like Shopify) using Amazon’s warehouse network. Sellers send their inventory to Amazon’s fulfillment centers (the same ones used for FBA), then use the Shopify MCF app to route Shopify orders to Amazon. Amazon picks, packs, and ships these orders, typically with Prime-like speed.

• Integration: Shopify offers an official “Amazon MCF and Buy with Prime” app. This free app connects your Shopify store to your Amazon seller account. It automatically maps SKUs and syncs inventory between Shopify and Amazon. After setup, any paid Shopify order can be imported into Amazon’s system for MCF. The integration provides real-time order status and inventory updates in Shopify. (Alternate third-party apps exist for MCF in other countries, but the Shopify app handles the U.S. by default.)
• Warehouse presence: Amazon MCF leverages Amazon’s extensive fulfillment centers worldwide. For Shopify merchants in the U.S., it uses Amazon’s U.S. FCs. Sellers in other countries can use Amazon’s local fulfillment networks via region-specific apps or partners. This effectively gives MCF a global footprint, although the Shopify MCF app officially supports U.S. and customers must have a U.S. seller account.
• Pricing model: MCF is pure pay-as-you-go. There are no monthly fees or subscriptions. You pay Amazon’s published fulfillment fees (based on item size/weight) and storage fees (based on cubic volume). Fulfillment fees are all-inclusive (pick, pack, ship) and drop up to 50% for multi-unit orders. For example, a small item might be a few dollars per order; large/long items can be tens of dollars. You also pay standard Amazon storage fees and any extra service fees (returns processing, labeling, remote delivery surcharges, etc.). Overall, costs align with FBA rates. All billing is “pay per unit”; there are no long-term contracts or hidden fees.
• CPG brand compatibility: MCF follows Amazon’s product rules. Any item prohibited on Amazon (hazardous materials, alcohol, prescription drugs, etc.) cannot be fulfilled by MCF. For allowed CPG products, MCF can handle most non-restricted consumer goods. Amazon also has special programs for refrigerated or high-value items, but those are separate from standard MCF. In practice, MCF is best for typical retail CPG (books, electronics, clothing, health & beauty, shelf-stable food).

Comparison of Top Shopify 3PLs (2025)

To summarize the key differences, the table below compares the top fulfillment partners for Shopify on integration, pricing, locations, and CPG support:

Final Thoughts

Selecting the best 3PL for Shopify requires balancing features and fit for your business. The “best” partner for a high-volume CPG brand might differ from that for a small boutique Shopify seller. You should use the criteria we discussed (seamless Shopify integration, strong support, clear pricing, suitable warehouse locations, and experience with your product category) as your compass. All the 3PLs profiled above integrate with Shopify to automate fulfillment (some are even officially part of Shopify’s network), but they have real differentiators in approach.

In 2025, Shopify sellers have more choices than ever for fulfillment. It’s worth doing due diligence: read reviews, ask about integration details, request a demo of their software, and get a detailed quote. A great Shopify logistics partner will be transparent and eager to address your questions around integration, support, and costs. By picking the right 3PL, you’ll gain a fulfillment team that can scale with you to ensure fast deliveries, happy customers, and ultimately, more freedom for you to focus on growing your Shopify store.