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Based on weighted criteria below
Low Pricing icon

Low Pricing (weighted 11%)

Zendesk

Zendesk offers 4 princing plans:

Essential:

$5/mo per agent when billed annually
or
$9/mo when billed month-to-month

Main features include:

Unlimited email addresses
Twitter and Facebook channels
Basic knowledge base
Agent Macros

Team:

$19/mo per agent when billed annually
or
$25/mo when billed month-to-month

Main features include:

All Essential features
Branded Help Center
Customer portal
Public Apps Marketplace

Proffessional:

$49/mo per agent when billed annually
or
$59/mo when billed month-to-month

All Team features
Multilingual content
Insights analytics
Custom private apps

Enterprise:

$99/mo per agent when billed annually
or
$125/mo when billed month-to-month

All Professional features
Custom agent roles
Multibrand support
Multiple schedules
Hourly Insights analytics

The 30-day free trial starts with the Professional plan. No credit card is required and there are no cancellation fees. If no payment method is added at the end of the trial period, the account is deleted 90 days after the trial expiration date.

Zendesk is a bit more pricey but for annual billing you'll get a 15% discount.

Intercom

With Intercom pricing is based on the total number of people you track and communicate with, not the number of agent seats your support team has. Be careful, pricing will automatically adjust as your business grows and you track more people.

There are two base plans for the customer support plan called Resolve:

Lite:

Pricing ranging from:

$49/mo for 250 people
to
$503/mo for 50.000 people

Main features include:

Multiple channels
Shared team inbox
Live profiles
Mobile apps

Standard:

Pricing ranging from:

$79/mo for 250 people
to
$810/mo for 50.000 people

Main features include:

Assign messages using rules
Integrations
Team member permissions
Unbranded Intercom Messenger and emails

There's a 14-day free trial that starts directly with the plan and number of people that you need. A credit card is required to start your trial. You will have a chance to confirm your subscription before starting. After your free trial ends, Intercom's products start at $49/mo, but if you cancel in the first 14 days you won't be charged.

The Intercom Platform shows you who your customers are and what they do in your web or mobile app, for free.

There are two more products besides Customer Support: Acquire (Intercom product for Live Chat) and Engage (Intercom product for marketing Automation). You can get the complete set starting from $61/mo.

Design icon

Design (weighted 11%)

Zendesk

Since August 2016 a new version of the agent/admin interface of Zendesk is available, with a more clean and modern design. You can choose from a selection of templates that will match your brand, or you can start creating your design from scratch.

Intercom

The design of the interface is fresh and clean and the user dashboard offers a lot of information. Once you login you'll notice that the interface is pretty intuitive and easy to use.

The communication features are also really good. One of the weakest points of intercom is that the design is not responsive, therefore accessing the service from mobile devices could be improved.

If you're looking to customize the interface to match your brand, go with Zendesk.

Features icon

Features (weighted 11%)

Zendesk

The Help Center is designed to give you a complete self-service support option (knowledge base). Users can use the information you are providing or turn to a community forum for answers.  Your Agents can also use the Help Center to solve tickets. You can deliver all the content in multiple languages.

Top features include: Unlimited email addresses, Twitter and Facebook channels, Knowledge base, Branded Help Center, Public Apps Marketplace, Multilingual content, Business hours & SLAs, Insights analytics, Multibrand support, Auditing & admin controls.

Intercom

Some of the key features include: Intercom Messenger, that will allow customers to contact you inside your web or mobile app; Customer profiles let's you save customer location, activity, and more, all in real time; Assignment Rules is a great feature that allows you to create rules to automatically assign conversations to the right team or teammate; with Saved replies you'll be able to respond to  questions with canned, yet personalized replies; tagging allows you to group related people or conversations with tags—search for them later; Typing indicators, read receipts, stickers, and emojis make conversations simple and engaging.

Backend Features icon

Backend Features (weighted 11%)

Zendesk

Zendesk will give you the option to transform your interface to match your brand. With familiar customization tools, you can easily tailor the look and feel.

There are five menu items on the left side of the screen:

First, a Home button gives you access to your dashboard, where you'll find a snapshot of your current configuration. On the Views section you'll find your unsolved tickets.

Next is the Reporting section, where you will get detailed snapshots of ticketing, agents, customers, self-service, and more. Last button on the bottom left corner will take you to your settings where you'll find all the fine-grained controls for your account.

The last button in the bottom left of the screen is a link to the Admin home page, here you'll find the tools you need to configure Zendesk.

Two more menu items can be found on the top right corner:

First (next to the search box) is a menu item that lets you select between the Support section and the Help Center. Next, if you click on your avatar you can access all your Profile Settings.

Intercom

All you conversations and team members can be accessed from the top left of the screen.

You can access your Support Insights by selecting the Support icon from the left-hand navigation bar and clicking ‘Insights.’

Your account settings can be accessed from the top right of you screen.

Team size icon

Team size (weighted 11%)

Zendesk

Without a doubt Zendesk is the most popular help desk sofware out there, this doesn’t mean that there is no competition. Using Zendesk if you have a small team would work fine, even tough . Zendesk will best suit you if you are planning to expand or you already own a large company that will require advanced features like advanced analytics and reporting, segmentation or retargeting.

Intercom

Intercom is packed with features but still has a clean and easy to use interface. Small business could definitely , The only thing making it less suitable for small teams is the high starting price which tends to scale if the volume of emails starts to grow.

Reports icon

Reports (weighted 11%)

Zendesk

Zendesk Reports are available for all plans and provide metrics such as daily ticket activity, service level agreement compliance, average resolution time, customer satisfaction, agent performance, ticket resolution time, and efficiency.

Insights provides advanced reporting and metrics but is available only for the Professional and Enterprise plans.

Intercom

Your support insights will show you data about your signed up users and visitors to your site.

You can see exactly if your support volume is increasing, if your team is responding fast enough to your users and leads, and who on your team is the busiest.

All your Support Insights get updated only once a day (midnight for your timezone).

Flexibility icon

Flexibility (weighted 11%)

Zendesk

Zendesk offers a built-in chat option (paid separately), a mobile app (both for iOS and Android) integrated apps so that you can offer fully scalable customer support. The Help Center gives you a lot of flexibility.

Intercom

iOS and Android apps will help you view, manage, and respond to customer conversations from your mobile device.

Live chat is also available as a separate product.

Building your own knowledge base is not supported at the moment. This is a bit of a letdown as you'll have to use third party apps to create a self help section.

Having an knowledge base can dramatically lift your site's customer experience, so if you're planning on building one go with LiveAgent.

Extensibility icon

Extensibility (weighted 11%)

Zendesk

Zendesk offers more than 350 integrations available, called apps. The apps are found in the Apps Marketplace with some of the most popular being: SalesForce, ZenCart, Magento, JIRA, TeamViewer, Drupal, Joomla, Wordpress, PlanBox, MailChimp, and 8X8. If you wish to create your own custom app, you can take advantage of Zendesk's API.

Intercom

There are only 41 integrations at the moment, but most of the popular online services are available: MailChimp, AWeber, Braintree, Shopify, Facebook, or Twitter.

If you're code savvy and you're really tied to a particular web service there is an API available for creating integrations.

If you need to have access to integrations right out the box, Zendesk is the big winner here.

Support icon

Support (weighted 11%)

Zendesk

Zendesk has a dedicated support section where you can access the knowledge base, Getting Started tutorials and the community forum.
If you can't find here the answers you need, or you just need to get in touch with them about pricing or billing, then you have all the options available: contact form, phone support (with separate phone numbers for different countries and time zones) and social media (if you're looking for a quick answer).

Intercom

Their support section is based on the Docs forum, where you can ask questions or read on related topics. The Intercom team will usually answer to all questions on this forum.

Once you login into your account, a live chat popup is available if you have questions that need quick answers.

They will also offer support by email, but no telephone numbers are listed for reaching out to the team.