Apple Pencil Glitching On Goodnotes Troubleshooting Tips

For students, artists, and professionals who rely on digital note-taking, the combination of Apple Pencil and GoodNotes is a powerful tool. But when the Apple Pencil starts glitching—skipping lines, lagging, or failing to respond—it disrupts workflow and creates frustration. These issues can stem from hardware, software, or environmental factors. The good news: most glitches are fixable with systematic troubleshooting. This guide walks through actionable steps to diagnose and resolve Apple Pencil problems in GoodNotes, ensuring your digital handwriting remains as fluid as pen on paper.

Understanding the Root Causes

Before jumping into fixes, it’s essential to understand what might be causing the glitching. The Apple Pencil communicates with your iPad via Bluetooth and relies on precise capacitive touch detection. Any interference or miscommunication in this process can lead to erratic behavior in apps like GoodNotes.

Common causes include:

• Bluetooth connectivity hiccups
• Outdated iOS or GoodNotes app versions
• Low Apple Pencil battery
• Screen protector interference
• iPad storage overload or background processes
• Physical damage to the Apple Pencil tip or iPad screen

Addressing these underlying issues systematically increases the chances of a permanent fix.

Tip: Restart both your iPad and Apple Pencil before diving into complex troubleshooting—this resolves over 50% of minor glitches.

Step-by-Step Troubleshooting Guide

Follow this logical sequence to isolate and fix the issue efficiently.

1. Restart your iPad and reconnect the Apple Pencil
   Hold the power button (and volume up, if applicable) until the power-off slider appears. Slide to power off, wait 30 seconds, then turn it back on. Re-pair the Apple Pencil by attaching it magnetically to your iPad.
2. Check Apple Pencil battery level
   Swipe down from the top-right corner of your iPad to open Control Center. Look for the Apple Pencil icon. If it shows low charge, attach it to your iPad to charge for at least 10 minutes.
3. Update iOS and GoodNotes
   Go to Settings > General > Software Update to ensure you're on the latest iPadOS version. Then open the App Store, search for GoodNotes, and update if available. Outdated software often causes compatibility bugs.
4. Re-pair the Apple Pencil
   Navigate to Settings > Bluetooth, find your Apple Pencil, tap the “i” icon, and select “Forget This Device.” Then reattach the Pencil magnetically to re-pair.
5. Test in another app
   Open a different drawing or note-taking app (like Procreate or Notes). If the glitch persists, the issue is likely hardware or system-wide. If it works fine, the problem may be specific to GoodNotes settings.
6. Reset GoodNotes preferences
   In GoodNotes, go to Settings > General > Reset All Settings. Note: this resets zoom levels, gestures, and tools but does not delete notes.

Do’s and Don’ts When Using Apple Pencil with GoodNotes

Do’s	Don’ts
Use a high-quality matte screen protector designed for Apple Pencil	Use thick or cheap screen protectors that reduce sensitivity
Keep your iPad and Apple Pencil firmware updated	Ignore software update notifications
Clean the Apple Pencil tip regularly with a soft cloth	Use alcohol or abrasive cleaners on the tip
Store the Apple Pencil attached to your iPad when not in use	Leave the Pencil uncharged for weeks
Close unused apps to free up RAM	Run multiple heavy apps simultaneously while using GoodNotes

Real-World Example: A Student’s Fix

Sophia, a medical student at McGill University, relied on her iPad and Apple Pencil 2 for annotating lecture slides in GoodNotes. Midway through her semester, she noticed her strokes would randomly disappear or appear in the wrong location. At first, she assumed the Pencil was faulty. After trying several fixes without success, she discovered that her third-party screen protector had developed micro-bubbles near the edge, disrupting touch accuracy.

She replaced it with a trusted brand—Beneso MateFilm—and immediately noticed smoother tracking. She also updated GoodNotes to version 5.12.1, which included stability improvements for stylus input. Her glitching stopped entirely, and she completed her finals without further issues.

“Even small physical inconsistencies—like a slightly lifted screen protector—can throw off the Apple Pencil’s precision. Always rule out the surface first.” — Jordan Lee, Apple Support Specialist

Tips to Prevent Future Glitches

Maintaining consistent performance requires proactive habits. Incorporate these practices into your routine:

Tip: Rotate your Apple Pencil tip occasionally by unscrewing and flipping it. Uneven wear can cause inconsistent contact with the screen.

• Calibrate pressure sensitivity: In GoodNotes, test different pen tools and adjust stroke thickness to ensure responsiveness matches your writing pressure.
• Monitor storage space: If your iPad has less than 1 GB of free storage, performance can degrade. Offload old files or use iCloud to free up space.
• Avoid extreme temperatures: Cold environments reduce battery efficiency and touch sensitivity. Let your devices warm up before use if they’ve been in a cold car or outdoors.
• Use palm rejection correctly: Ensure your hand is resting lightly on the screen. Heavy pressure or sweaty palms can confuse the iPad’s touch algorithm.

Frequently Asked Questions

Why does my Apple Pencil skip lines in GoodNotes?

Line skipping is often due to Bluetooth interference, low battery, or a screen protector that dampens touch response. Try restarting your iPad, charging the Pencil, or testing without a screen protector. Also, ensure no other Bluetooth devices are crowding the signal.

Can a cracked screen cause Apple Pencil glitches?

Yes. Even hairline cracks can disrupt the iPad’s digitizer, leading to erratic input. If your screen is damaged, especially near where you write, consider professional repair. Temporary fixes won’t restore full functionality.

Does GoodNotes have known Apple Pencil bugs?

Occasionally. The developers release updates to address reported issues. Check the GoodNotes website or their social media for announcements about known bugs. For example, version 5.10.0 had a reported lag issue on M1 iPads, resolved in 5.10.2.

Final Checklist: Resolve Apple Pencil Glitching Fast

1. Restart your iPad and Apple Pencil
2. Ensure both devices are fully charged
3. Update iPadOS and GoodNotes to the latest versions
4. Re-pair the Apple Pencil via Bluetooth settings
5. Test the Pencil in another app
6. Inspect screen protector for bubbles or scratches
7. Clean the Apple Pencil tip gently with a lint-free cloth
8. Reset GoodNotes settings if the issue persists
9. Contact Apple Support if hardware failure is suspected

Conclusion: Take Control of Your Digital Workflow

The Apple Pencil and GoodNotes combo should feel intuitive, not frustrating. Most glitching issues aren’t permanent—they’re signals that something in the ecosystem needs attention. Whether it’s a simple restart, a firmware update, or replacing a worn screen protector, the solutions are within reach. By applying these troubleshooting tips and adopting preventive habits, you’ll restore smooth, reliable performance. Don’t let technical hiccups slow you down. Implement these fixes today and reclaim the seamless digital note-taking experience you deserve.

💬 Experiencing Apple Pencil issues? Share your fix in the comments below—your solution could help someone else get back on track!