I have used them both in Website Design and am comfortable with them. Each one has some Plus and Minus Points. Here are some of the Differences.
Zen Cart vs WooCommerce:
Zen Cart and Woo Commerce are very different. Zen Cart is an open source shopping cart system, whereas Woo Commerce is a WordPress plugin. With one of these two choices, you can put up an ecommerce store, start selling product online and grow your business. However, they won’t both fit for every business.
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Zen Cart

As an open source system using PHP and MySQL, you will need hosting that allows you to use both of these for your website. Most standard shared and VPS hosting companies will give you the ability to use PHP and MySQL. Since this is an open source system, it’s free to download, which makes it a great choice if you’re on a budget. Some shopping cart systems are expensive to use, but not Zen Cart.
Within the system, you can use a template system to customize the look and function of your store. There are also many different free and premium themes available for Zen Cart making it easy to change the look of your online store. If you’re looking a shopping cart system above and beyond the other open source choices, Zen Cart is the one. It’s very similar to OS Commerce, but it’s more advanced.
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WooCommerce

With the Woo Commerce plugin, you need to use a WordPress website or it won’t do you any good. This plugin allows you to use many different types of reporting, dashboard widgets, coupons and more. You can integrate multiple payment methods and you can set the shipping, tax, product and inventory however you prefer.
Along with the many features, you can also take advantage of the many extensions and themes provided by the WooThemes website. Some of the extensions are free, while others commercial. Overall, you can use the Woo Commerce system free of charge, but some of the things you might need will come with a small fee.
Additional features give you the ability to integrate dynamic pricing, Use add-ons, choose per product shipping rates and even choose table rate shipping choices. The system is completely customizable and you get the ability to make your store work and look the way you prefer.
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Who is Zen Cart For?

Zen Cart will fit with beginners and advanced users looking to make only a small investment. If you want to manage your store yourself, this is a great choice. Of course, it works with any website using PHP and MySQL. You don’t have to use WordPress for your website to use Zen Cart, but it’s an option.
Zen Cart works great for those needing to provide a catalog of many different products and allows you to use categories, category images and product images. There are many advantages to Zen Cart, but those using WordPress may prefer Woo Commerce instead.
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Who is Woo Commerce For?

The major limitation to Woo Commerce is the fact that it only works with WordPress website. If you’re not using WordPress for your website, Woo Commerce is worthless to you. However, WordPress users can download the plugin free of charge, use the custom themes and create the store of their dreams easier than with most other shopping cart choices.
If you’re a beginner or advanced user and you prefer WordPress for your website, Woo Commerce is one of the best options for your needs. Of course, you can use another shopping cart choice, but one of the major benefits of Woo Commerce for WordPress users is that it’s created specifically for WordPress.
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The Best Choice Between Zen Cart vs. Woo Commerce

Narrowing down your choices for the right ecommerce solution is important. When you’ve narrowed the choice down to Zen Cart or Woo Commerce, you need to choose the right one for your specific needs. These are both great choices, but the WordPress user will have a harder decision since Woo Commerce works with WordPress.

Looking at Zen Cart vs. Woo Commerce allows you to see the advantages and disadvantages. If you’re using WordPress, Woo Commerce is the right choice. However, if you’re not using WordPress, Zen Cart will be the better choice out of the two systems. Neither system is better than the other, but they work better for certain types of websites. Make sure you match the right choice to your business because the wrong choice could waste your time.

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