calibre Table of Contents Missing After Conversion: How to Fix It

When a converted e-book opens normally but its navigation panel is empty, disabled, or missing, the problem is usually not the visible contents page. It is the book's metadata or navigation table of contents, which reading applications and devices use for chapter navigation. The most common causes are an input file with no usable navigation data, chapter headings that calibre cannot detect, conversion settings that preserve a broken source table of contents, or a device that is opening an older copy of the book. This guide shows you how to isolate the cause, repair the navigation structure, and verify the result without reinstalling calibre or changing unrelated settings.

1. Confirm the Symptom With a Small Safe Test

Start by confirming exactly what is missing. An e-book can contain two different kinds of contents:

• Navigation or metadata table of contents: The chapter list opened through a viewer's navigation button or a device's Go to menu.
• Inline contents page: A normal page inside the book containing chapter names and, sometimes, clickable links.

A book may have either one, both, or neither. Seeing a contents page near the beginning does not prove that the book contains a working navigation table of contents. Likewise, a working navigation panel does not require a visible contents page.

1.1 Test the converted file in the calibre viewer

1. Select the converted format in calibre.
2. Open that specific format in the calibre E-book viewer.
3. Open the viewer controls and select the Table of Contents button.
4. Check whether chapter entries appear and whether several entries jump to the correct locations.

If the viewer displays a usable chapter list, the conversion probably succeeded. Stop changing conversion settings and investigate the copy sent to the device, the selected device format, or the device's reader software.

If the viewer's table of contents is empty or unavailable, the problem is inside the converted file. Continue with the conversion and editing checks below.

1.2 Make sure you opened the new output

calibre can store several formats under one library entry, including EPUB, AZW3, MOBI, and PDF. Confirm that you are testing the newly converted format rather than the original file or an older exported copy. After reconverting, check the job completion time and reopen the format from the calibre library.

For a device test, remove the old device copy before sending the corrected book again. If two editions share the same title and author, a reader may continue opening the older edition. Success means the calibre viewer and the device both show the same chapter list.

2. Check Structure Detection and Table of Contents Settings

During conversion, calibre can preserve an existing metadata table of contents or generate one from the document's structure. A missing result often means the input contains no valid navigation data and calibre did not recognize the chapter headings.

2.1 Inspect the source before forcing automatic generation

If the source is EPUB or AZW3, open it in the calibre viewer first and check its navigation panel. If the source already has a correct table of contents, calibre normally prefers that information during conversion. Avoid selecting options that replace it unless the existing table is incomplete or broken.

If the source table is empty or incorrect, automatic generation may be appropriate. In the conversion dialog, open the Table of Contents section and review the option that forces calibre to use an automatically generated table of contents. Use it when the source navigation data is unusable but the document has detectable headings.

Success looks like a populated navigation panel containing sensible chapter names in the output. Once it works, stop changing detection expressions or thresholds.

2.2 Check whether the chapter headings are real headings

Chapter titles that merely look large or bold may not be structurally marked as headings. For example, a word processor document might format every chapter title as a large normal paragraph rather than applying Heading 1 or Heading 2. calibre then has less reliable information from which to build navigation entries.

For DOCX sources, apply built-in heading styles to chapter titles in the original document and convert it again. Use Heading 1 for major chapters and Heading 2 for sections when that hierarchy is appropriate. Do not apply heading styles to decorative text, running headers, or every paragraph.

For HTML-based sources, proper <h1>, <h2>, and <h3> elements provide clearer structure than styled <p> or <div> elements. Success means the generated navigation entries correspond to actual chapters rather than random bold text.

2.3 Review Structure detection

Open the conversion dialog and select Structure detection. calibre uses chapter detection rules to identify chapter boundaries in the intermediate XHTML created during conversion. Detected chapters can then be included in the automatically generated table of contents.

The default rule recognizes many common heading patterns, but it cannot anticipate every source. It may miss chapters named only with numbers, Roman numerals, dates, or unconventional labels. It can also miss headings represented by ordinary paragraphs with custom classes.

Do not change page-break rules merely because navigation is missing. Chapter detection and page-break detection are related but not identical. Concentrate on the chapter detection field and the Table of Contents options that use detected chapters.

2.4 Use simple XPath expressions when necessary

XPath tells calibre which elements should become chapters or table of contents entries. You do not need to master XPath to solve common cases. Begin with the narrowest simple expression that matches the source structure:

• //h:h1 selects all first-level HTML headings.
• //h:h2 selects all second-level HTML headings.
• //*[@class='chapter'] selects elements whose class is exactly chapter.
• //h:h2[re:test(., 'chapter|section', 'i')] selects second-level headings containing chapter or section, without regard to case.

Use the XPath wizard in the conversion dialog where available. Avoid copying a class such as calibre1 from the converted output into a detection rule. Conversion can rewrite CSS class names, so expressions should be based on the input structure. Tag names and visible heading text are often safer targets.

In the Table of Contents section, Level 1, Level 2, and Level 3 expressions can define the hierarchy directly. For example, Level 1 can select chapter headings while Level 2 selects subsection headings. Test one level first. Add more levels only after the primary chapter list works.

2.5 Check options that suppress or replace entries

Several settings can produce an unexpectedly empty or incomplete result:

• Do not add detected chapters: Disable this when you expect detected chapter headings to populate the table of contents.
• Force use of auto-generated Table of Contents: Enable it only when replacing a missing or defective source table of contents.
• Level expressions: A custom Level 1 expression takes precedence over simpler automatic detection. An expression that matches nothing can therefore produce no useful entries.
• Table of contents filter: An overly broad filter can remove legitimate entries.
• Chapter threshold and link fallback: These affect whether links found in the source are added when too few chapters are detected.

If you previously experimented with these fields, temporarily restore them to defaults and test again. Then make one controlled change. Success means the output contains the expected chapters without duplicate or irrelevant entries.

3. Repair EPUB or AZW3 Navigation With Edit Book

For EPUB and AZW3 files, calibre's Edit book tool is often the fastest and most reliable repair method. It lets you inspect and change the navigation table directly instead of repeatedly guessing at conversion rules.

3.1 Open the Table of Contents editor

1. Select the EPUB or AZW3 format in the library.
2. Choose Edit book.
3. Open Tools, Table of Contents, and Edit Table of Contents.
4. Review the entries and their destinations.

If the list is empty, generate entries from headings, links, or files. Generating from headings is usually best when chapters use proper heading elements. Generating from files can be useful when every chapter occupies a separate HTML file but lacks consistent headings.

After generation, remove front matter or decorative headings that should not appear. Arrange entries in reading order and correct their hierarchy. You can also change an entry's destination by selecting the correct location in the preview.

Save the book and open it in the calibre viewer. Success means the navigation panel opens, each tested entry reaches the correct chapter, and the hierarchy is sensible. At that point, do not reconvert the repaired file unless another format is required.

3.2 Run Check book when entries do not work

In Edit book, use Tools and Check book to look for broken links, malformed markup, missing files, or package errors. These problems can leave visible chapter text intact while breaking navigation destinations.

Review each suggested repair before applying it, and keep the editor's checkpoint so changes can be reverted. A successful repair produces a clean or materially improved check result and working table of contents destinations in the viewer.

3.3 Keep the inline contents page separate

The Edit book tool can insert an inline table of contents based on the existing navigation table. This is optional and does not replace the need to create navigation entries first. If the device's navigation menu is empty, inserting only a visible page is not the primary fix.

Create or repair the metadata table of contents first. Add an inline page afterward only if the reading experience or publishing requirements call for one.

4. Account for MOBI and Reader-Specific Behavior

MOBI handles navigation differently from EPUB and AZW3. calibre may represent MOBI's navigation table through an additional inline table of contents, commonly placed near the end of the book. That generated section supports navigation behavior that MOBI cannot implement as cleanly as newer formats.

In MOBI Output settings, avoid disabling the generated inline table of contents unless you have a specific, tested reason. A book can contain what appear to be two contents lists because one is the author's visible page and the other represents MOBI navigation.

When the target device supports AZW3 or EPUB appropriately, testing one of those formats can help identify a MOBI-specific limitation. However, use a format officially supported by the target application, device, or delivery method.

4.1 Compare calibre viewer behavior with device behavior

If the output works in the calibre viewer but not on the device, conversion settings are unlikely to be the first problem. Check the following:

• The device received the corrected format rather than an older MOBI or EPUB.
• The device is opening the sideloaded copy you updated.
• The device's reading application supports navigation for that format.
• The book was safely ejected and fully indexed after transfer.
• The selected Send to device format matches the one tested in calibre.

USB mode, filesystem permissions, or a read-only mount matter when they prevent the corrected file from replacing the old one. They do not normally remove a table of contents from a file that was transferred successfully.

4.2 Rule out stale delivery paths

Email delivery and the calibre Content server do not usually rebuild an e-book's internal navigation. However, they can expose the wrong stored format or a cached copy. Download the exact format from the server and test that downloaded file in the calibre viewer. For email delivery, verify which format calibre selected and compare it with the locally tested output.

Firewall and network settings are relevant only if the transfer fails, stops early, or serves an old file. Antivirus interference or operating system permissions are relevant if calibre cannot write the conversion output, update the library format, or save Edit book changes. Check the conversion job result before investigating network or security software.

4.3 Be careful with cloud-synced libraries

A live calibre library should not be treated like an ordinary cloud-synced document folder while calibre is changing files. Sync conflicts can restore an older format or interfere with library updates. If the library is inside a synchronization service, pause synchronization during a controlled test and work from a local temporary library.

Do not delete the main library. The goal is to determine whether the corrected output remains corrected when stored and opened locally.

5. Use Conversion Debug Output and Job Details

Logs are useful when chapter detection should work but does not. They show whether the problem began in the source, during structure detection, or while building the final format.

5.1 Read the conversion job details

After conversion, open the completed Jobs entry and view its details. Look for warnings or errors related to input processing, malformed HTML, table of contents generation, or output creation. A completed job does not guarantee that chapter headings were detected, so combine the log with a viewer test.

If the job converted a different input format than expected, return to the conversion dialog and inspect the input format shown in the upper-left area. calibre may have multiple source formats available for the same library record.

5.2 Generate conversion debug files

The conversion dialog provides a debug option that writes intermediate conversion stages to a folder. The most useful folders for this symptom are:

• input: Shows what the input plugin extracted from the source.
• parsed: Shows the normalized XHTML used for structure detection.
• structure: Shows the content after structure detection.
• processed: Shows the content shortly before the output plugin creates the e-book.

Open the relevant HTML files and search for a known chapter title. Check which element surrounds it. If a chapter is an <h2>, a simple heading XPath may work. If it is a paragraph with a distinctive class, create a rule for that input structure. If the title is absent or garbled in the input stage, changing table of contents settings cannot restore information that the input plugin never received.

5.3 Use command-line debugging only when needed

Most users will not need calibre-debug. It can launch calibre components with diagnostic output, and its device-driver option can help when calibre does not detect a connected reader. Device detection debugging is appropriate when no transfer is occurring, not when the same file transfers successfully but lacks navigation everywhere.

Use command-line debugging after the viewer, editor, conversion settings, and job details have narrowed the problem. It should not be the first response to a missing table of contents.

6. Run a Clean Temporary Test Before Reinstalling

Reinstalling calibre rarely repairs a table of contents stored inside one book. A clean test provides better evidence and does not endanger the library.

1. Copy the original source file to a normal local folder with write access.
2. Add the copy to a temporary calibre library.
3. Disable nonessential conversion or file-type plugins temporarily if they participate in the workflow.
4. Convert to EPUB using default settings.
5. Open the output in the calibre viewer and inspect its navigation panel.
6. If navigation is missing, repeat the conversion with one appropriate chapter or Level 1 XPath rule.
7. If necessary, repair the EPUB directly with Edit book and test again.

If default conversion works in the temporary library, the original book-specific conversion settings, a plugin, a stale source format, or the original library environment is influencing the result. calibre remembers conversion settings for individual books, and those settings can take precedence over general defaults.

If the temporary conversion also fails, inspect the source structure. Poorly tagged HTML, scanned PDFs, image-only pages, and documents whose chapter titles are ordinary paragraphs may require source cleanup or manual table of contents creation.

Stop once the output works in the calibre viewer. Only then send that exact file to the device. This separates book repair from transfer troubleshooting.

7. Quick Fix Checklist

• Confirm that the missing feature is the navigation table of contents, not only an inline page.
• Open the exact converted format in the calibre viewer.
• Check whether the source EPUB or AZW3 already contains working navigation data.
• Use real Heading styles in DOCX source documents.
• Review Structure detection and remove custom XPath rules that match nothing.
• Ensure detected chapters are allowed into the generated table of contents.
• Force automatic generation only when the source table is absent or defective.
• Use simple Level 1 XPath such as //h:h1 or //h:h2 when appropriate.
• Repair EPUB or AZW3 directly with Edit book and its Table of Contents tool.
• Run Check book to find broken internal links or package errors.
• Do not confuse MOBI's generated inline navigation section with an unwanted duplicate.
• Delete or replace stale device copies before retesting.
• Check conversion job details and debug output before reinstalling calibre.
• Test in a temporary local library before modifying the main library.

8. Frequently Asked Questions

8.1 Why is there a visible contents page but no navigation menu?

The visible page may be ordinary book content. Unless the e-book also defines navigation metadata, the viewer or device has no structured chapter list to display. Generate or edit the metadata table of contents, then test it through the calibre viewer's Table of Contents control.

8.2 Why did calibre create no entries from my chapter titles?

The titles may be visually formatted paragraphs rather than structural headings, or the current chapter detection expression may not match them. Inspect the intermediate XHTML with conversion debug output. Apply proper heading styles at the source or create a simple XPath expression that matches the actual input elements.

8.3 Should I enable Force use of auto-generated Table of Contents?

Enable it when the source has no navigation table or contains a broken one that calibre would otherwise preserve. Leave it disabled when the source table is already accurate. After conversion, test several entries and stop changing settings if they work.

8.4 Can I fix the table of contents without converting again?

Yes. For EPUB and AZW3, open Edit book and use Tools, Table of Contents, Edit Table of Contents. Generate entries from headings, links, or files, correct their destinations, save the book, and verify it in the calibre viewer.

8.5 Why does the table of contents work in calibre but not on my device?

The device may be opening an older copy, receiving a different format, or using reader software with limited support for that format. Remove the old copy, send the exact file tested in calibre, safely eject the device, and test again. Do not keep changing conversion settings when the converted file already works locally.

8.6 Is calibre not working if only one book has this problem?

Usually not. A problem limited to one title normally points to that source file's structure, saved per-book conversion settings, or internal navigation data. Test another well-structured document or create a small DOCX with Heading 1 chapter titles. If that conversion produces working navigation, calibre's conversion system is functioning and the original source needs targeted repair.