Writing a thesis that includes published or accepted journal papers sounds straightforward — until formatting begins.

If you’re preparing a thesis by publication (or a hybrid thesis), you may encounter problems such as:

  • Page numbers that don’t match the Table of Contents
  • Blurry figures after copying journal content into Word
  • Word becoming slow or crashing due to large files
  • Inconsistent formatting across chapters

After testing multiple approaches, I found that the most reliable solution is:

Prepare the structure in Word, but insert published papers only at the PDF stage.

This guide describes a workflow that produces a clean, submission-ready thesis with consistent page numbering and high-quality journal pages.

When to Use This Method

This workflow is especially useful if:

  • Your thesis includes published or accepted papers
  • You are required to keep the journal layout unchanged
  • You want consistent page numbering across the entire thesis
  • You want to avoid formatting problems close to submission

Workflow Overview

The process consists of two stages:

Stage 1 – Word

  • Create sections
  • Set page numbering
  • Leave placeholder pages for journal chapters

Stage 2 – PDF

  • Export the thesis
  • Remove placeholder pages
  • Insert journal PDFs
  • Add final page numbers

This separation keeps Word stable and ensures the journal pages remain high quality.

Stage 1 – Prepare the Thesis in Word

Assume your thesis text is complete and only formatting remains.

If a chapter is a published paper, insert blank placeholder pages where the paper will later be added.

Step 1. Create Three Sections

Insert Section Breaks (Next Page) at:

  • End of the cover page
  • End of the Table of Contents

You should have:

Section Content Page style
1 Cover page No number
2 Front matter Roman numerals (i, ii, iii…)
3 Main chapters Arabic numerals (1, 2, 3…)

Step 2. Set Page Numbers

Front matter

  • Insert page numbers
  • Format as i, ii, iii…
  • Start at i

Main chapters

  • Insert page numbers
  • Format as 1, 2, 3…
  • Start at 1

Step 3. Update the Table of Contents

Update the Table of Contents so all page numbers are correct.

Step 4. Check Page Number Font

Double-click a page number and note:

  • Font family
  • Font size

Tip: Some PDF tools only support even font sizes. Using 10 pt often avoids issues later.

Step 5. Temporarily Remove Main-Chapter Numbers

Before exporting:

  1. Go to Chapter 1
  2. Double-click the footer
  3. Turn off “Link to Previous”
  4. Delete the page number

This removes numbering from all main chapters.

Important:
Do not update the Table of Contents again after this step.

Export the document as PDF.

Stage 2 – Finalize in a PDF Editor

Open the exported file using a PDF editor (e.g., Adobe Acrobat, PDFgear, or any tool that supports page insertion and numbering).

Step 1. Remove Placeholder Pages

Delete the blank pages that were reserved for the published paper.

Step 2. Insert the Journal PDF

Insert the official journal PDF at the correct position.

This preserves:

  • Original layout
  • Fonts and formatting
  • Figure quality
  • Publisher requirements

Step 3. Add Final Page Numbers

Use the PDF editor’s page numbering feature:

  • Style: 1, 2, 3…
  • Start number: 1
  • Apply only to the main chapter range
  • Match the font and size used in Word

Make sure numbering begins from the page where Chapter 1 actually starts.

Save the final file — your hybrid thesis is now ready.

Common Mistakes to Avoid

  • Updating the Table of Contents after removing page numbers in Word
  • Copy-pasting journal content instead of inserting the official PDF
  • Adding page numbers in both Word and PDF (causes duplication)
  • Forgetting to keep a backup before exporting

Why This Workflow Works

This approach separates responsibilities:

Tool Role
Word Structure, sections, ToC
PDF editor Final layout and numbering

Benefits:

  • Stable performance in Word
  • High-quality journal pages
  • Consistent page numbering
  • Minimal last-minute formatting stress

Final Thoughts

Formatting a thesis by publication often becomes unexpectedly time-consuming near submission.
Setting up a reliable workflow early can save hours of troubleshooting — and a lot of unnecessary stress.

If you’re currently in the final stage of your PhD, I hope this guide makes the process a little smoother.