Note: This article includes information specific to the Japanese e-commerce market (e.g., Japan-specific services, regulations, or customs). Some details may not apply outside Japan.
When opening an online shop, many people wonder whether to choose an independent online store or an online marketplace.
Independent online stores make it easier to express your brand and use customer data, while online marketplaces help you tap into existing search demand. Choose based on your products, existing sources of traffic, and operational setup, and use both as needed.
This article compares the differences between independent online stores and online marketplaces, and explains the pros and cons of each, the costs, and how to choose for each type of merchant.
What are independent online stores and online marketplaces?
Independent online stores and online marketplaces both let you sell products online, but they differ in how stores are operated.
What is an independent online store?
An independent online store is an e-commerce site that a company or individual builds and operates on its own. You can use services such as Shopify, BASE, or makeshop, packaged e-commerce software, or custom development.
You can tailor your site's design and sales methods to your business, making it easier to express your brand identity. You will, however, need to attract customers through SEO, social media, online advertising, and other channels.
For details on how to build an independent online store, see the article below.
What is an online marketplace?
An online marketplace brings together multiple stores and sellers to sell products online. Examples include Rakuten Ichiba, Amazon, and Yahoo! Shopping.
Online marketplaces already have many users, so shoppers may discover your products even if your business is not well known. Their payment and order management systems also make it relatively straightforward to start selling.
However, there are also many competing products inside the marketplace, along with costs such as selling fees and restrictions on how you operate.
For the features of major online marketplaces and how to choose among them, see the article below.
Comparing the differences between independent online stores and online marketplaces
The main differences between an independent online store and an online marketplace are as follows.
| Point of comparison | Independent online store | Online marketplace |
|---|---|---|
| Where you sell | Your own e-commerce site | Shop and product pages inside the marketplace |
| Customer acquisition | You acquire customers yourself | You can tap into the marketplace's existing audience |
| Initial cost | JPY 0 and up (varies widely depending on the build method) | JPY 0 and up (varies by marketplace) |
| Operating costs | System usage fees, payment fees, advertising costs, and more | Store fees, sales-related fees, advertising costs, and more |
| Design flexibility | Relatively high | There are restrictions based on the marketplace's specifications |
| Use of customer data | Easier to collect and use your own customer data | The scope of use is limited |
| Branding | Easier to express your brand identity | You need to differentiate inside the marketplace |
| Price competition | Easier to communicate your unique value | Easily compared with competing products |
Note: Costs, features, and operational restrictions differ depending on the service you use.
The biggest differences are how you attract customers and build relationships with them.
On an online marketplace, visitors may discover your products. With an independent online store, you need to attract customers yourself, but you can more readily use data such as purchase history to encourage repeat purchases and ongoing sales.
Pros and cons of an independent online store
An independent online store offers flexible store operations, but you need to attract customers and establish an operational setup.
Pros of an independent online store
The main pros of an independent online store are the following three.
Easier branding
You can tailor your site's design and product pages to your business, making it easier to express your brand identity. Product pages also give you more scope to communicate features and value beyond price.
Easier use of customer data
You can analyze purchase history and customer attributes and use them for promotions such as email marketing and member campaigns. This makes it easier to build ongoing customer relationships, encourage repeat purchases, and increase LTV (customer lifetime value).
More flexibility in sales methods
You can more readily adopt sales methods tailored to your products and customers, such as product bundles, subscriptions, and your own membership program. The available features and customization options depend on the e-commerce platform you use.
Cons of an independent online store
The main cons of an independent online store are the following two.
You need to acquire customers yourself
Publishing an e-commerce site alone is unlikely to bring enough traffic. You need to keep working on SEO, social media, online advertising, and other activities to raise awareness.
Operations require a lot of work
Your business needs to take the lead on site improvements, promotional planning, and customer analysis. You may also need specialist staff or outside support, which can increase the operational burden.
Pros and cons of an online marketplace
Online marketplaces offer access to an existing audience, but you need to consider fees and operational restrictions.
Pros of an online marketplace
The main pros of an online marketplace are the following three.
Access to an existing audience
People searching within the marketplace may discover your products. Products commonly searched for by model number or product name are particularly well suited to tapping into existing demand.
Reassurance for customers
A well-known marketplace's payment systems and customer services can help reassure first-time customers.
Easy to start selling
Product listings, order management, payments, and other systems are already available, so you can start selling without developing your own system. However, you may need to complete an approval process and configure various settings.
Cons of an online marketplace
The main cons of an online marketplace are the following three.
Selling fees
Depending on the marketplace, you may pay store fees, sales-related fees, and costs for points programs. Even as sales rise, these costs may leave insufficient profit.
Exposure to price competition
Competing products appear in the same marketplace, making it easier for shoppers to compare prices, reviews, and other factors. Price competition may be particularly intense when several stores sell the same product.
Flexibility of operations is limited
Site design, promotions, customer data use, and other activities must follow the marketplace's terms and specifications. Changes to those terms or fees also affect your business.
Which costs less, an independent online store or an online marketplace?
Operating costs for an independent online store and an online marketplace differ depending on the service you use and your sales volume. It is important to compare not only the monthly fee, but also fees that are charged based on sales.
A comparison of the initial cost, fixed monthly cost, and main costs that vary with sales for representative services is as follows.
| Service (plan) | Initial cost | Fixed monthly cost | Main costs that vary with sales |
|---|---|---|---|
| Shopify (Basic) | JPY 0 | JPY 3,650 Note: Monthly equivalent of annual billing | Shopify Payments domestic card payment fee: 3.55% and up |
| Rakuten Ichiba (がんばれ！プラン) | JPY 60,000 | JPY 25,000 Note: Annual lump-sum payment | System usage fee: 3.5 to 7.0% (depends on the device, sales, and other factors) Rakuten Pay usage fee: 2.5 to 3.5% Costs of funding reward points, and other fees |
| Amazon (Professional selling plan) | JPY 0 | JPY 4,900 | Referral fees of 5 to 15.4% in many categories |
| Yahoo! Shopping | JPY 0 | JPY 10,000 | Sales royalty: 2.5% Payment service usage fee Costs of funding reward points at 1% or more, and other fees |
Note: Pricing for Japan, confirmed on October 29, 2026. For Shopify, the platform's initial cost is listed, and outsourcing costs for producing the site and similar costs are not included. Fixed costs and initial costs for each marketplace exclude tax. Charges and fees differ depending on the plan, product category, payment method, and other factors.
Note: Shopify's 3.55% and up is the rate for domestic card payments when you use Shopify Payments on Basic. The rate differs by card type. If you use an external payment service on its own or in combination, different conditions apply, such as a transaction fee, additional fees, and more.
Note: Rakuten Ichiba also charges separate fees, including a system usage fee for transaction safety and convenience equal to 0.1% of monthly sales. Monthly store fees are scheduled to change from February 1, 2027. The monthly rate for がんばれ！プラン, paid in an annual lump sum, will be JPY 34,000 (excluding tax). Check the official notice for the application and billing dates for existing contracts.
Note: Yahoo! Shopping began charging a monthly system usage fee and sales royalty in September 2026. From January 2027, orders purchased through the cart in LINE's shopping tab are scheduled to incur a fee of 2 to 4% of the product selling price, excluding tax.
With an independent online store, you do not pay a marketplace store fee, but you may pay payment processing fees and other sales-based fees depending on the service you use. These may be lower than a marketplace's sales-related fees, but you also need to budget for customer acquisition advertising, apps, and other costs. Sales volume alone does not determine which option is more economical.
An online marketplace gives you access to an existing audience, but advertising may still be necessary depending on your visibility within the marketplace and the competitive environment. Whether customer acquisition costs are lower than for an independent online store depends on your products and sales methods.
When judging which is less expensive, compare the total cost, including not only the monthly fee and selling fees, but also advertising costs, labor costs, shipping costs, and more.
Pricing sources: Shopify pricing, Shopify Payments fees, Rakuten Ichiba store fees, Rakuten Ichiba fee revision, Amazon selling fees, Yahoo! Shopping store fees, Yahoo! Shopping new plan
Which should you choose, an independent online store or an online marketplace?
Choose an independent online store or an online marketplace based on the products you sell, your sales strategy, your ability to attract customers, and other factors.
Merchants suited to an online marketplace
An online marketplace is suited to merchants such as the following.
- Your name recognition is low, and you want to use search demand inside the marketplace
- You sell products that are easy to compare and search for by model number or product name, such as home appliances and daily necessities
- You want to start selling first, without building your own e-commerce site
Being able to use existing purchase demand is a strength, but you also need to check the number of competing products and the selling fees.
Merchants suited to an independent online store
An independent online store is suited to merchants such as the following.
- You sell original products and want to communicate your brand identity
- You already have a certain existing audience, such as social media or a physical store
- You want to use customer data and work on developing repeat customers and increasing LTV (customer lifetime value)
In particular, when you want to carefully communicate product features and your brand story, a highly flexible independent online store is suitable.
However, just because a product is original does not mean it is unsuited to an online marketplace. Depending on demand inside the marketplace and the competitive environment, it can become a strong sales channel.
Merchants suited to using both
You do not need to choose only one. For example, you can use an online marketplace to reach new customers and an independent online store to communicate your brand's appeal and strengthen programs for repeat customers.
Businesses already making sales on a marketplace can also open an independent online store to expand their sales channels. Using both offers the strengths of each, but it also means managing more stores. Establish the operational setup before taking this on.
Points to watch when using an independent online store and an online marketplace together
When using an independent online store and an online marketplace together, pay particular attention to inventory and order management.
For example, if you sell the same product in multiple stores, delays in inventory updates can lead to overselling. Management becomes more complex as you add channels, so consider a centralized inventory and order management system as needed.
You also need to consider pricing and promotional policy for each channel. Actions such as directing customers inside the marketplace to your independent online store may be restricted by each marketplace's terms, so check the rules in advance.
Consider Shopify for an independent online store
Shopify is also an option for merchants who want to build a site that fits their brand and keep adding the features and sales channels they need. You can build an e-commerce site that fits your brand by using a wide range of design themes, and, by adding apps, you can also extend features such as subscriptions and displaying reviews.
Shopify's website explains the features available for building a store and selling products.
Image source: Shopify
Through sales channels and apps, you can also connect with social media such as Instagram and with some online marketplaces such as Amazon. You can expand your sales channels while checking the terms of use and the supported countries and regions.
Feature source: Shopify sales channels (confirmed on October 29, 2026)
If you are considering opening an e-commerce site on Shopify, please also refer to the article below.
Choose sales channels that fit your company and grow your e-commerce business
This article explained the differences between independent online stores and online marketplaces. Independent online stores and online marketplaces differ mainly in customer acquisition methods, costs, flexibility of operations, and more.
An online marketplace is likely a good fit for merchants who want to sell by using an existing existing audience. An independent online store, on the other hand, is a sales method suited to merchants who value branding and the use of customer data.
There is also a way to use both, not only to choose one or the other. Choose appropriate sales channels based on your product characteristics, your ability to attract customers, and your operating setup.
