How to Annotate a PDF in Chrome

Ever tried to quickly mark up a PDF, only to end up downloading a clunky online tool, waiting for it to open, and juggling between windows just to highlight a sentence?

Yeah, same.

That is where Web Highlights changes the game. It is a lightweight Chrome annotation extension that lets you highlight, comment, and tag any PDF task right inside your browser. It offers multiple annotation options with no extra software, switching tabs, or bloated tools.

In this guide, I will walk you through how to annotate a PDF in Chrome using Web Highlights, from installing the extension to organizing your highlights and exporting them to tools like Notion or Obsidian. If you are a student, researcher, or just someone who reads a lot of PDFs online, this is for you.

Understanding PDF Annotation

PDF annotation is all about interacting with a document. It includes highlighting key points, adding comments, marking diagrams, or leaving quick reminders for later. Whether underlining a definition, tagging a quote, or drawing attention to a confusing chart, document annotation tools help you stay organized while reading.

With PDF annotations, everything is easier:

• You don’t have to re-read full pages—just scan your notes through highlights.
• You can filter and search by tags or keywords.
• Save bookmarks for later.
• It’s great for collaborating or prepping for meetings, exams, or research reviews.

And yes, you can also annotate local PDFs from your computer; you’ll just need to make one small adjustment in your browser settings to allow file access. Here's a quick guide on how to highlight local PDFs using Web Highlights.

Doing all this inside Chrome means you skip the annoying part: no file downloads, no switching between a PDF viewer and a notes app. With a PDF annotation Chrome extension like Web Highlights, you just open a PDF link, start annotating, and everything is stored in one place.

It’s an effective PDF annotation without breaking your reading flow, and that is what makes it practical.

Setting Up Web Highlights for PDF Annotation

Before you start highlighting or adding notes, you'll need to set up Web Highlights properly. It only takes a few steps to turn Chrome into a full PDF annotation tool, and no separate apps or complicated software are required.

The first thing you need to do is install the Web Highlights extension from the Chrome Web Store. You can also simply click on the “Add to Chrome” button that appears on their webpage, which takes you directly to the Chrome web store.

It takes less than a minute and installs like any other browser extension. Once added, you’ll see the Web Highlights icon in your Chrome toolbar.

Bonus Tip: Make sure to pin the extension for easy access. 

To unlock all features like image annotation, sync across devices, and the ability to export your PDF annotations to tools like Notion or Obsidian, you’ll need to create an account or sign in. The free version already gives you plenty of flexibility, but a Web Highlights account lets you fully utilise its advanced PDF annotation tool capabilities.

Once you're signed in, you’re ready to use Web Highlights as your go-to Chrome annotation extension. Next, let's move on to how to annotate a PDF in Chrome.

Annotating PDFs Directly in Chrome

Once you’ve set up Web Highlights, annotating a PDF in Chrome becomes second nature. Let’s break it down step by step:

Step 1: Open the PDF in Web Highlights 

Open any PDF on your browser and then set it up on Web Highlights. 

You can do this by clicking the “Highlight this PDF” pop-up on the top right of your PDF, or you can simply click on the Web Highlights extension icon available in your extension bar. 

Once you do this, the PDF format automatically opens in the Web Highlights app, which is ready to be used as a PDF annotation tool.

With a simple and user-friendly interface, Web Highlights makes it easier to carry out different annotation options. 

Step 2: Start highlighting 

To highlight PDF text, just click and drag over the section you want to mark. A small pop-up gives you the highlight option, allowing you to choose from multiple highlight colors. These color choices aren’t just for looks. They help you visually separate ideas, quotes, key points, or to-dos at a glance. 

Tip: Use the keyboard shortcut (Alt+S) for faster navigation, making it easy to annotate longer PDF documents without breaking your reading flow. Web Highlights also gives you the option to customize your keyboard shortcuts. 

Step 3: Select format or add notes

Web Highlights supports a range of PDF annotation features and in different text formats, too. You can format highlights into bullet points, numbered lists, headings (H1, H2), quotes, and code. This makes it work well for both structured documents and plain-text PDFs. Whether you’re annotating a formal report or a lecture handout, the extension makes it easy to apply consistent formatting.

Need to leave a thought, summary, or reminder next to a highlighted section? 

Just right-click on the highlight and select “Take a note.” This allows you to jot down anything in a simple text box, which automatically gets stored in the sidebar on the left. 

What makes this even better is that all your PDF annotations, both highlights and notes, stay saved under your account. If you're logged in, everything syncs to the cloud, and you can review your annotations from any device.

Step 4: Undo, Redo, and Edit Annotations

Made a mistake while highlighting? No problem. Web Highlights includes quick editing annotations tools so you can undo, redo, or change anything without restarting your work.

At the top of the highlight popup, you’ll see simple controls. Just click the dustbin icon to delete your last action if you change your mind. If you want to edit a note or switch a highlight color, just click on the existing annotation to update it. Whether it’s a sticky note, a text selection, or an image markup, everything remains editable.

The goal here is an effective annotation you can tweak and manage as your work evolves.

Organizing and Tagging Your Annotations

Highlighting a PDF is just the first step; organizing those annotations makes them useful later.

With Web Highlights, you can apply topic tags to every highlight or note. Think of tags like labels: “Definitions,” “Research evidence,” “Key Points,” or anything else that helps you group similar annotations. These tags let you filter and find specific content instantly, which is a lifesaver when you're skimming through dozens of PDF documents.

The tagging system is flexible and straightforward to use. You can add multiple tags to the same highlight and update them anytime. 

By clicking on the “tags” icon, you can easily access all your tags on one page. This acts as a collection, helping you create an efficient PDF workflow. 

Combined with the ability to highlight in PDF, add notes, and tag them clearly, these annotation functions make Web Highlights more than just a text annotation tool. If you’ve been wondering how to annotate a PDF in Chrome without downloading extra software, this is it. 

Exporting PDF Annotations to Knowledge Platforms

Web Highlights isn’t just a PDF annotation tool. It also helps you move your notes into the apps where you actually use them. Here’s how:

1. Export to Notion

With one click, send your highlights to Notion. Each annotation becomes a database row, complete with your note, tags, and a page reference to the original PDF. Ideal for organizing research or building a reading tracker.

2. Export to Obsidian / Markdown

Prefer working in Obsidian? You can export your annotations as an .md file with proper formatting and backlinks to the original PDF. This fits well with workflows that rely on Markdown or connected notes.

3. Other Export Formats

Web Highlights also supports HTML, CSV, and Capacities export. Use CSV for spreadsheets and bulk editing, HTML for clean previews, or Capacities if that’s your tool of choice. 

Reviewing and Managing Annotations Over Time

Knowing how to annotate a PDF in Chrome is only useful if you can find and use your notes later. Web Highlights makes it easy to review and manage annotations without digging through old files or re-reading full documents.

You can bulk-edit tags, delete outdated notes, or merge duplicate highlights from your dashboard. This is great for keeping your research tidy and your annotation process focused.

There’s also a handy email “Snooze” reminder feature. You can set reminders to revisit specific PDFs or annotations later, which is perfect for long-term projects or papers you must follow up on. Instead of forgetting about a useful PDF version you skimmed last week, Web Highlights brings it back to your inbox at just the right time.

Tips for Efficient PDF Annotation

If you're working with a lot of PDF documents, small habits can make a big difference in how effective your annotations are.

One easy tip is to use color coding for priority. Mark important highlights in pink, possible references in yellow, and general notes in blue. It is a simple way to visually separate what’s urgent from what’s just “good to know,” making reviewing faster later.

Web Highlights also includes a built-in Reader Mode, which removes distractions like ads, pop-ups, and clutter from web pages and online PDFs. If you’re trying to focus on reading and note-taking without noise, Reader Mode is worth enabling. Web Highlights lets you adjust the font size, switch between light and dark themes, and tweak text alignment, making long reading sessions way more comfortable.

You’ll see only the core content, which works seamlessly with the annotation features you already use. Here’s how to use Reader Mode.

Another clever trick: let your annotations sync on Wi-Fi, and then work offline while you travel or study somewhere without the internet. Web Highlights queues your changes and syncs everything once you’re back online. So your highlights, sticky notes, and tags are always up to date, even if you’re on a plane or in a dead zone.

Final Thoughts

Using a browser-based tool like Web Highlights means you don’t waste time opening heavy software or juggling between apps. It simplifies how you annotate PDFs in Chrome, keeps your notes searchable, and connects smoothly with tools like Notion, Obsidian, and Markdown.

Now that you know how to annotate a PDF in Chrome without extra hassle, give it a try and see how it fits into your workflow. It's one of those document annotation tools that just makes sense.

Install Web Highlights today!

Frequently Asked Questions

1. Does Web Highlights store the PDF itself or just the annotations?

Web Highlights does not store the PDF file itself. It only saves your PDF annotations, tags, and notes securely under your account. This way, you can reopen the same file later and continue working using your preferred annotating tools.

2. Can I annotate password-protected PDFs?

Currently, most PDF annotation Chrome extensions, including Web Highlights, do not support annotation on password-protected files due to browser-level restrictions. You’ll need to unlock the PDF first to use the annotation features.

3. Is image annotation available on the free plan?

Image annotation, where you can draw boxes around charts or visuals, is a premium feature. The free plan gives you full access to basic annotation tools like text highlights, sticky notes, and tagging, but image markup is available in the Pro version.

 4. How do I share an annotated PDF with colleagues?

After you annotate your PDF in Chrome, you can export your highlights and notes to tools like Notion, Obsidian, or Markdown and then share them. Alternatively, you can send your teammates the PDF link if it’s hosted online. They can view annotations if they’re also using Web Highlights or receive your notes via export.

5. Will annotations sync between Chrome and Edge?

Yes, your annotations sync across browsers as long as you're signed into your Web Highlights account. Whether using Chrome, Edge, or another Chromium-based browser, your annotations, tags, and notes stay connected through the cloud, making it easy to continue your work anywhere.