You've merged your PDFs. You open the result, and... ugh. Page 3 is landscape when everything else is portrait. The font on page 7 looks completely different. Page 12 has weird spacing. Page 20 is rotated sideways. What should have been a simple merge turned into a formatting disaster.
I've seen this happen more times than I can count, and I've learned that most of these problems are preventable if you know what to look for. Let me walk you through the common issues that make merged PDFs look weird, why they happen, and—most importantly—how to fix or prevent them.
The Page Size Problem
This is probably the most common issue. You merge a letter-sized document with an A4 document, and suddenly your PDF has pages of different sizes. When you view it, some pages look normal, others are too wide or too narrow, and printing becomes a nightmare.
Why it happens: PDFs preserve the original page size of each document. If Document A was created as letter size (8.5" x 11") and Document B was created as A4 (8.27" x 11.69"), the merged PDF will have both sizes. There's no automatic resizing.
How to fix it: You have a few options. The easiest is to resize all pages to match before merging. Our Merge PDF tool preserves page sizes as they are, so if you need uniform sizes, you'll need to resize pages first using a PDF editor, then merge.
Alternatively, if you have the source files, recreate the PDFs with consistent page sizes. Export everything as the same size from the original software.
Prevention: When creating PDFs you know you'll merge later, use consistent page sizes from the start. It's easier to match sizes at creation than to fix them later.
The Font Disaster
You merge documents, and suddenly some pages have different fonts. Text that was Times New Roman is now Arial. Headers that matched perfectly now look completely different. It's jarring and unprofessional.
Why it happens: Fonts can be embedded or not embedded in PDFs. If a font isn't embedded and your system doesn't have it, the PDF viewer substitutes a different font. When you merge, if some PDFs have embedded fonts and others don't, you get inconsistency.
Also, if you're merging PDFs created by different people using different software, they might have used different default fonts or font settings.
How to fix it: This is harder to fix after merging. You can try to re-embed fonts, but it's not always possible. The best solution is usually to go back to the source files and recreate the PDFs with consistent fonts.
If you can't do that, at least make sure fonts are embedded in all your source PDFs before merging. That way, even if fonts differ, they'll display consistently.
Prevention: Establish font standards before creating documents you'll merge. Use the same fonts, the same sizes, the same styles. It sounds obvious, but you'd be surprised how often people don't think about this until it's too late.
The Rotation Issue
You merge documents, and some pages are rotated. Page 5 is sideways. Page 12 is upside down. It looks unprofessional and is annoying to read.
Why it happens: Pages can have rotation metadata in PDFs. If someone rotated a page in the original document (maybe to fix a scan), that rotation is preserved. When you merge, rotated pages stay rotated.
Also, scanned documents often have rotation issues. If pages were scanned at different orientations, they'll have different rotations in the PDF.
How to fix it: Use our Rotate PDF tool to fix rotated pages before merging. Go through your source files, identify rotated pages, and rotate them to the correct orientation. Then use our Merge PDF tool to combine them. It's easier to fix rotations before merging than after.
Better yet, fix rotations in the source files before merging. That way you only have to do it once, and your merged PDF will be perfect from the start.
Prevention: When scanning or creating PDFs, make sure all pages are oriented correctly from the start. Check each page before finalizing the document.
The Spacing and Layout Problems
You merge documents, and suddenly spacing is off. Margins don't match. Text alignment is inconsistent. Headers and footers are in different positions. The document looks pieced together rather than cohesive.
Why it happens: Different documents have different margin settings, different header/footer configurations, and different layout styles. When you merge, all of that gets preserved, creating inconsistency.
Also, if documents were created with different software (Word vs Google Docs vs a design tool), they might have different default spacing and layout settings.
How to fix it: This is one of the hardest problems to fix after merging. You can't easily change margins or spacing in a merged PDF without specialized tools.
Your best bet is usually to go back to source files and standardize margins, headers, and footers before creating PDFs. If that's not possible, you might need to use a PDF editor to manually adjust pages, which is time-consuming.
Prevention: Use consistent formatting standards. Same margins, same header/footer style, same spacing. Create a template if you're merging documents regularly.
The Page Numbering Nightmare
You merge documents, and page numbers are all over the place. The first document had pages 1-10, the second had pages 1-15, and now your merged PDF has two page 1s, two page 2s, etc. Or page numbers continue incorrectly (page 10, then page 16 instead of page 11).
Why it happens: Page numbers in PDFs are usually part of the page content, not metadata. When you merge, each document's page numbers stay as they were. There's no automatic renumbering.
How to fix it: You have a few options. If page numbers are in headers or footers, you might be able to remove them and add new ones using a PDF editor. But this is manual work.
Some advanced PDF tools can renumber pages, but it's not common in basic merging tools. You might need to use a dedicated PDF editor.
Prevention: If you know you'll merge documents, consider not including page numbers in individual files. Add page numbers after merging, so they're consistent throughout.
Or, if you must have page numbers in source files, plan the numbering. If Document A is 10 pages, start Document B at page 11.
The Color and Image Issues
You merge documents, and some pages look different. Colors are off. Images are pixelated or low quality. Some pages are grayscale when others are color.
Why it happens: Different PDFs might have different color profiles, different image compression settings, or different color modes. When merged, these differences become obvious.
Also, if some documents were created for print (CMYK color) and others for screen (RGB color), you'll see color differences.
How to fix it: This is hard to fix after merging. You'd need to adjust color profiles and image settings, which usually requires going back to source files.
Prevention: Use consistent color settings when creating PDFs. If you're merging documents, make sure they all use the same color mode (RGB for screen, CMYK for print, or grayscale if that's appropriate).
The Bookmark and Navigation Problems
Your original PDFs had bookmarks or a table of contents. After merging, they're gone, or they point to the wrong pages, or they're duplicated.
Why it happens: Not all merging tools handle bookmarks well. Some preserve them, some don't. Some try to preserve them but mess up the page references.
How to fix it: If bookmarks are important, you might need to recreate them after merging. Some PDF editors let you add bookmarks manually.
Or use a merging tool that specifically handles bookmarks well. Check tool documentation to see how they handle navigation elements.
Prevention: If bookmarks are critical, test your merging tool with a small sample first. See how it handles bookmarks before merging your important documents.
The Metadata Mess
You merge documents, and the file properties are wrong. Author shows as one person when it should be another. Creation date is off. Title doesn't match.
Why it happens: When you merge, the resulting PDF usually inherits metadata from one of the source files (often the first one). If your source files have different metadata, the merged file might have incorrect or mixed information.
How to fix it: Update the metadata after merging. Most PDF tools let you edit document properties. Set the correct author, title, creation date, etc.
Prevention: Standardize metadata in source files before merging. Or at least make sure the first file in your merge has the correct metadata, since that's often what gets used.
How to Prevent These Problems
The best way to deal with weird merged PDFs is to prevent the problems in the first place. Here's my checklist:
- **Check page sizes** - Make sure all documents use the same page size before merging.
- **Check page orientation** - Make sure all pages are oriented correctly (no rotations).
- **Standardize fonts** - Use the same fonts, or at least make sure fonts are embedded.
- **Match formatting** - Use consistent margins, headers, footers, and spacing.
- **Plan page numbering** - Either don't include page numbers in source files, or plan the numbering sequence.
- **Check color settings** - Use consistent color modes and profiles.
- **Test bookmarks** - If navigation is important, test how your tool handles bookmarks.
- **Review metadata** - Make sure source file metadata is correct, or plan to update it after merging.
- **Use our Merge PDF tool** - Our [Merge PDF tool](../merge) shows file thumbnails so you can verify the order before merging. Check that files are in the right order and everything looks right.
- **Keep source files** - Don't delete originals until you've verified the merged file is correct.
Quick Fixes for Common Issues
If you've already merged and have problems, here are quick fixes:
Different page sizes: Use a PDF editor to resize pages to match. It's tedious but works.
Rotated pages: Rotate them back using your PDF tool's rotation feature.
Font issues: If fonts aren't embedded, you might be able to embed them. Otherwise, you might need to recreate from source.
Page numbers: Remove old page numbers and add new ones, or use a tool that can renumber automatically.
Bookmarks: Recreate them manually, or use a tool that handles bookmarks better.
Metadata: Edit document properties to correct information.
When to Start Over
Sometimes, fixing a merged PDF is more work than starting over. If you have source files and the problems are extensive, it's often faster to:
- Fix issues in source files
- Recreate PDFs with consistent settings
- Merge again
I know it's frustrating to redo work, but sometimes it's the most efficient solution. I've learned to ask myself: "Will fixing this take longer than redoing it?" If the answer is yes, I start over.
Final Thoughts
Merged PDFs look weird when source documents aren't consistent. The solution is usually to standardize before merging, not to fix after. Take time to check your source files, match their settings, and preview the merge result. A few minutes of preparation saves hours of fixing problems.
And remember: not every merge needs to be perfect. If you're merging internal documents that won't be shared, minor inconsistencies might be fine. But if you're creating something for clients, customers, or submission, take the time to get it right. The difference between a professional document and a messy one is often just a bit of attention to detail before you hit that merge button.
Ready to merge your PDFs? Try our Merge PDF tool now. Upload multiple PDF files, drag to reorder them, and merge them into one document. Our tool preserves formatting and page sizes, so your merged PDF will look professional. It's free, works in your browser, and keeps your files private.
