How to Merge Multiple Excel & CSV Files Into One (Free Tool + Steps)

To merge multiple Excel files into one, put every .xlsx and .csv file in a single folder and run a free command-line tool called Excel/CSV Merger, which combines them into one clean spreadsheet in seconds. It automatically lines up columns that don't match, labels every row with the file it came from, and can remove duplicate rows — no copy-pasting and no manual cleanup.

The problem: combining many spreadsheets by hand

Almost every office job produces the same headache: a folder full of spreadsheets that need to become one. Monthly sales exports, form responses split across files, reports from different team members, data pulled from separate systems — each arrives as its own .xlsx or .csv.

The usual "solution" is to open each file, copy the rows, and paste them into a master sheet. This is slow, and it silently goes wrong the moment two files have different columns or column orders. Rows land in the wrong place, headers get duplicated, and you lose track of which file a record came from. On 30 or 40 files, it's an afternoon gone.

What is Excel/CSV Merger?

Excel/CSV Merger is a free, open-source command-line tool that combines every Excel and CSV file in a folder into one clean file. It's written in Python and released under the MIT license, so anyone can use it at work or in their own projects at no cost.

Instead of copy-pasting, you point it at a folder and it does four things automatically:

• Reads every .csv, .xlsx and .xls file in the folder.
• Aligns mismatched columns by keeping the union of all column names.
• Tags each row with a source_file column.
• Optionally removes duplicate rows with a single flag.

How to install the tool (2 minutes)

You need Python 3.9 or newer. Then clone the repository and install its two dependencies:

git clone https://github.com/Synth88Labs/excel-tool-merger.git
cd excel-tool-merger
pip install -r requirements.txt

That's the whole setup. The tool uses only pandas and openpyxl — both trusted, widely used Python libraries.

Get Excel/CSV Merger on GitHub (free)

How to merge multiple Excel files into one — step by step

Once installed, combining a folder of files is a single command. Here's the full workflow.

Step 1 — Put your files in one folder

Collect every spreadsheet you want to combine into a single folder, for example ./reports. They can be a mix of .csv, .xlsx and .xls files — you don't need to make them match first.

Step 2 — Run the merge command

Point the tool at that folder and name your output file:

python merge_excel.py ./reports -o combined.xlsx

The tool prints each file it reads with its row and column count, then saves one merged workbook called combined.xlsx.

Step 3 — Remove duplicates (optional)

If the same rows appear in more than one file, add the --dedupe flag to drop them:

python merge_excel.py ./reports -o combined.xlsx --dedupe

Step 4 — Include sub-folders or output CSV (optional)

Use --recursive to also pull files from sub-folders, and end the output name in .csv if you'd rather have a CSV:

python merge_excel.py ./data -o everything.csv --recursive

Merging Excel files with different columns

This is where manual copy-paste fails and the tool shines. Say January has the columns id, customer, amount and February adds a region column. Excel/CSV Merger keeps the union of all columns: the final file has id, customer, amount, region, and the January rows simply show a blank region instead of throwing an error or shifting data into the wrong column.

Here's what that looks like with real data:

Real work use cases

People use a folder merger like this for everyday tasks such as:

• Monthly and quarterly reporting — combine 12 monthly sales exports into one annual file for a pivot table.
• Consolidating team submissions — merge spreadsheets from different colleagues or branches, keeping the source_file tag to track who sent what.
• Cleaning up data exports — many systems export data in batches; this stitches them back into one dataset.
• Survey and form responses — combine response files that were downloaded separately.
• Preparing data for analysis — get one tidy file before loading it into Excel, Power BI, or a Python notebook.

Merger tool vs. manual copy-paste vs. Power Query

There's more than one way to combine spreadsheets. Here's an honest comparison so you can pick the right one for the job.

Power Query is a great built-in option if you want to stay inside Excel. A standalone tool wins when you're combining large folders, mixing CSV and Excel, don't have Excel installed, or want to run the same job on a schedule.

Common mistakes to avoid

• Merging files with inconsistent headers. "Amount", "amount" and "Amt" are treated as three different columns. Standardize header names before merging for the cleanest result.
• Forgetting the source column. Once rows are combined, you can't always tell where a record came from — keep the source_file tag on (it's on by default) unless you have a reason to drop it.
• Assuming duplicates are gone. Deduplication only removes fully identical rows and only when you pass --dedupe. Near-duplicates (same order, different formatting) still need review.
• Mixing the wrong sheets. For multi-sheet Excel files, the tool reads the first sheet by default. Use --sheet "SheetName" to target the right tab.
• Leaving a workbook open. While it skips lock files, it's still safest to close Excel before merging so every file is fully saved.

Frequently asked questions

Summary

Combining a folder of spreadsheets by hand is slow and breaks whenever columns don't match. Excel/CSV Merger merges multiple Excel and CSV files into one clean file with a single command — aligning columns automatically, tagging each row's source, and optionally removing duplicates. It's free, open-source, and works without Excel installed.

Download Excel/CSV Merger free on GitHub