How to Clone SD Cards with Multiple Partitions: A Complete User Guide
6 November 2025 Specialist of Customer Service Dept.
Last update by Olivia Brown at 17 November 2025
Summary
Learn how to clone SD cards with multiple partitions safely and efficiently. This step-by-step guide covers the best tools and methods for preserving boot and data partitions, ensuring a flawless SD card duplication for any device.
Working with an SD card that’s split into multiple partitions—whether from a Raspberry Pi setup, a MiSTer FPGA project, Nintendo Switch game storage, camera files, drone footage, or even Android phone expansions—can be tricky. If you need to clone that card to back it up, move to a larger one, or duplicate it across devices, you’re in the right place.
Embedded systems often divide SD cards into partitions like FAT32 for boot, ext4 for the root file system, or hidden recovery areas. Since Windows and macOS don’t always recognize these layouts, a simple file copy won’t preserve everything.
This guide shows you reliable ways to clone the entire card—keeping every partition intact and bootable. We’ll start with beginner-friendly tools and move up to advanced options, so you can avoid data loss and get the job done right.
| Scenario | Key Characteristics & Notes | Boot Support Required? | Partition Scheme & Max Partitions | Recommended Methods |
|---|---|---|---|---|
| Raspberry Pi Setup | FAT32 boot + ext4 root + optional data/log partitions. | ✅ Yes | MBR (default for Pi firmware). Max: 4 primary (or 3 + 1 extended with logicals). | PiClone (Pi-specific), Renee Becca, dd (Linux), Clonezilla for advanced multi-partition handling. |
| MiSTer FPGA Project | Multiple partitions for Linux base, cores, and user data. | ✅ Yes | MBR (commonly used). Max: 4 primary (extended partition allows more). | Clonezilla, dd for raw cloning, Renee Becca. |
| Nintendo Switch Games (SD Expansion) | exFAT/FAT32 partitions for game data only. | ❌ No | MBR (Switch expects MBR). Max: 4 primary. | Balena Etcher, dd for exact copy, Renee Becca for easy backup/restore. |
| Camera Files (Professional Use) | Usually single FAT32/exFAT; some cameras add metadata partitions. | ❌ No | MBR (most cameras). Max: 4 primary. | Renee Becca or commercial cloning software (easy GUI), dd for raw sector copy. |
| Drone Footage | FAT32/exFAT, may include hidden telemetry/firmware partitions. | ❌ Usually no | MBR (drone firmware expects it). Max: 4 primary. | Clonezilla, dd for exact sector copy, Renee Becca for user-friendly cloning. |
| Android Phone Storage Expansion | FAT32/exFAT for media + hidden/system partitions. | ❌ No | MBR on most microSD cards; GPT possible on newer Android versions. Max: 4 primary (MBR) or up to 128 partitions (GPT). | Clonezilla (multi-partition aware), dd for raw cloning, Renee Becca or commercial tools for GUI-based cloning, Balena Etcher. |
Some articles suggest that you can use Win32DiskImager to copy SD cards with multiple partitions, but in reality, it can’t directly handle multi-partition setups. It only recognizes and works with a single mountable partition or the full device path (like \.\PhysicalDriveX), not multiple partitions.
When you clone an SD card onto a larger one, you usually end up with unused space. There are two straightforward ways to deal with it:
1. Smart Clone with Partition Resize
Use cloning software with “smart clone” features (like Renee Becca). It can automatically adjust partition sizes during the cloning process so the new card uses all available space right away.
2. Create a New Partition After Cloning
If you’ve already cloned the card and see leftover space, simply create a new partition in that free area. You can do this with partitioning tools, or directly in your system’s built‑in disk management (Windows, macOS, or embedded Linux environments).
3. The Manual Way : Resize after cloning
If you use a tool that does a 1:1 copy (like dd or Balena Etcher), you must resize the partition after the clone is complete.
- On Raspberry Pi: Boot the new card in your Pi, run sudo raspi-config, and go to “Advanced Options” > “Expand Filesystem”.
- On a PC: Use a partition manager like GParted (a free bootable tool) to see and expand the Linux (ext4) partition into the unallocated space. Windows Disk Management can do this to extend FAT32/exFAT/NTFS partitions.
Now that you know which tools work best for different scenarios, let’s walk through the actual cloning process. We’ll start with beginner‑friendly methods and move toward more advanced techniques. These steps apply whether you’re backing up a Raspberry Pi image, duplicating a Nintendo Switch card, or migrating storage for drones and cameras.
Tip: Always connect both your source and target SD cards using reliable card readers before you begin. This helps avoid detection issues.
This guide focuses on cloning the entire SD card, including all partitions, for a complete replica. If you only need certain partitions (like just the data partition), you can adapt the steps or use partition‑specific modes in the tools mentioned. For example, when upgrading a MiSTer FPGA card, full cloning ensures both the boot and game partitions are preserved.
🖥️ OS: Supports Windows
⚙️ Functions: ✅ Full disk cloning, ✅ Partition-specific cloning, ✅ Image creation and restoration, ✅ System migration
Renee Becca is a top-rated Windows tool for easily cloning multi-partition SD cards. Its straightforward interface is ideal for all skill levels, handling complex setups from devices like a Raspberry Pi or Android.
The software supports full disk cloning, partition-specific cloning, and system migration. Key features include adjustable partition sizing (perfect for upgrading to a larger card) and cloning only used space (great for SSDs).
Renee Becca – Safe and Quick System Migration to SSD
Automatic 4K alignment Improves SSD performance during system migration.
Support GPT and MBR Automatically adapt to the suitable partition format.
Support NTFS and FAT32 Redeploy various files in different file systems.
Back up quickly Back up files at up to 3,000MB/min.
Overall backup schedule Support system redeployment/system backup/partition backup/disk backup/disk clone.
Automatic 4K alignment Improve SSD performance
Support GPT and MBR Intelligently adapt to a partition format
Support NTFS and FAT32 Redeploy files in different file systems
As a real-world example, imagine you’re setting up multiple Raspberry Pi units for a home automation project. Using Renee Becca, you can clone your configured 64GB SD card to several 128GB ones in batches, adjusting partitions to fill the extra space automatically.
Advantages:
- Simple, clear interface that's easy to navigate
- Multiple cloning options to fit your needs, like full disk or partitions
- Supports resizing partitions during clone for larger targets
- Fast speeds and automatic backups for peace of mind
- Free for non-Windows disk cloning
Disadvantages:
- Windows-only, so Mac/Linux users need alternatives
- Advanced features might require the full version after trial
Step 1: Connect your SD cards to your PC with SD card reader.
Step 2: Download, install, and run Renee Becca on your PC.
In the main interface, head to the “Clone” column and select “Hard Disk Clone/Clone System Disk“.
Step 3: In the pop-up window, pick your source SD card as the original disk and the target SD card as the destination.
If the target is larger, drag the partition boundaries with your mouse to resize and use the extra space—super handy for upgrades.
To create an exact copy of the original SD card and ensure the clone is bootable, make sure to select the “Copy all sectors” option.
Step 4: Double-check everything, then hit “Clone” to start. The process is quick, and it verifies data to avoid errors. Once done, eject both cards safely.
If you want to backup your SD card, please head to Disk/Partition backup.
How to make full use of the remaining space
When cloning to a larger SD card, Renee Becca lets you resize partitions during the process. If you skipped that step, you can still create a new partition in the unused space using your system’s disk management tools—whether on Windows (diskmgmt.msc), macOS (Disk Utility), or Linux.
If you need to create a new partition in Windows, FAT32 partition format is recommended.
This method with Renee Becca is straightforward and minimizes risks, making it ideal for most users. If you’re looking for a free alternative, let’s move on to SD Card Copier next.
Renee Becca – Safe and Quick System Migration to SSD
Automatic 4K alignment Improves SSD performance during system migration.
Support GPT and MBR Automatically adapt to the suitable partition format.
Support NTFS and FAT32 Redeploy various files in different file systems.
Back up quickly Back up files at up to 3,000MB/min.
Overall backup schedule Support system redeployment/system backup/partition backup/disk backup/disk clone.
Automatic 4K alignment Improve SSD performance
Support GPT and MBR Intelligently adapt to a partition format
Support NTFS and FAT32 Redeploy files in different file systems
🖥️ OS: Applies only to Linux-based Pi OS
⚙️ Functions: SD card cloning
SD Card Copier (GUI) and PiClone (CLI) are Raspberry Pi-tailored tools for cloning SD cards with multiple partitions, perfect for Pi users in education or IoT projects where you duplicate setups across boards. Integrated in Raspbian, they automatically resize for larger targets and handle Pi’s unique boot/ext4 setups. Use them directly on a running Pi with a card reader. In 2025, they’re updated for Pi 5, aiding cluster builds.
Advantages:
- Official Pi tools, optimized for Raspbian
- Automatic resizing for upgrades
- No external PC needed
- Free and simple
- Handles Pi-specific partitions flawlessly
Disadvantages:
- Requires a running Pi setup
- GUI may glitch on remote access
- Not for non-Pi devices
- Limited to Linux-based Pi OS
- Slower for very large cards
Step 1: On your Pi, open SD Card Copier from the menu or run PiClone in terminal.
Step 2: Select source (internal SD) and target (via reader), then start copy. It adjusts sizes.
Step 3: Wait for completion and verify boot.
How to make full use of the remaining space
If you cloned to a larger card and didn’t resize during the process, you can still expand partitions using gparted or Raspberry Pi’s built-in partitioning tools. This ensures you’re not wasting valuable storage.
These tools are niche but indispensable for Raspberry Pi enthusiasts. If you’re looking for a better solution, let’s wrap up with Balena Etcher.
🖥️ OS: Supports Windows, Mac, and Linux
⚙️ Functions: flashing image files (requires a separate tool to generate the .img) and cloning SD cards (1:1 clone).
For users who switch between Windows, macOS, and Linux, Balena Etcher provides a free, graphical way to clone SD cards with multiple partitions. Balena Etcher is especially handy for direct card-to-image cloning in scenarios like drone enthusiasts backing up flight data cards or Android users expanding phone storage.
It’s flash-focused, validating clones automatically to catch errors, and supports various file systems without hiccups. In 2025 updates, Etcher added better multi-partition handling, making it great for Raspberry Pi clusters where you clone one configured card to many.
Advantages:
- Free and works on Windows/Mac/Linux
- Automatic validation reduces errors
- User-friendly with minimal steps
- Handles unrecognized partitions well
- No installation needed for Etcher portable
Disadvantages:
- No direct partition editing or resizing
- Etcher doesn't create .img files by default (focuses on flashing)
- Disk Utility is Mac-only
- Slower for very large cards
- Limited to basic clones without extras like scheduling
Step 1: Download and run it from official site (https://etcher.balena.io/).
Step 2: In the source selection menu, choose “Clone Drive.”
Step 3: Click the target selection menu, select your target SD Card.
How to make full use of the remaining space
Balena Etcher doesn’t support resizing partitions when cloning an SD card. To manage any leftover space after cloning to a larger card, you’ll need to use your system’s built-in tools: On Windows, use Disk Management (diskmgmt.msc); On macOS, use Disk Utility; On Linux, use tools like gparted or fdisk. These utilities let you expand existing partitions or create new ones to fully utilize the extra space.
These free GUI options bridge platforms nicely. If you want more control with paid features, let’s explore EaseUS Disk Copy or 4DDiG Partition Manager.
🖥️ OS: Supports Windows
⚙️ Functions: Full disk cloning, partition-specific cloning
EaseUS Disk Copy and 4DDiG Partition Manager are premium Windows tools excelling in mid-level cloning of SD cards with multiple partitions, suited for users like photographers migrating camera cards or gamers duplicating Switch setups. EaseUS offers sector-by-sector cloning for exact replicas, with options to autofit layouts on larger targets—perfect when upgrading from 16GB to 64GB without manual tweaks.
4DDiG adds recovery features, making it robust for faulty cards. Both support various file systems and provide previews, reducing surprises. In a 2025 case, IT admins used EaseUS for batch-cloning Android SD extensions in offices, saving hours. These aren’t free but offer trials and reliability over open-source alternatives.
Advantages:
- Automatic layout adjustments for different sizes
- Supports selective partition cloning
- Fast and stable with error checks
- User-friendly previews
- Additional tools like recovery in 4DDiG
Disadvantages:
- Requires payment for full features
- Windows-focused, less cross-platform
- Overwrites targets without backup prompts
- Can be resource-heavy on older PCs
- Trials have limitations
These commercial picks add polish for frequent users. For command-line precision, turn to the dd command next.
Renee Becca – Safe and Quick System Migration to SSD
Automatic 4K alignment Improves SSD performance during system migration.
Support GPT and MBR Automatically adapt to the suitable partition format.
Support NTFS and FAT32 Redeploy various files in different file systems.
Back up quickly Back up files at up to 3,000MB/min.
Overall backup schedule Support system redeployment/system backup/partition backup/disk backup/disk clone.
Automatic 4K alignment Improve SSD performance
Support GPT and MBR Intelligently adapt to a partition format
Support NTFS and FAT32 Redeploy files in different file systems
For power users who need precise, bit-level control over the cloning process, command-line tools offer unmatched flexibility and reliability. Let’s start with one of the most powerful and widely available options: dd.
🖥️ OS: Supports Windows, Mac, and Linux
⚙️ Functions: Cloning SD card
The dd command is a built-in Linux/Mac CLI tool for bit-for-bit cloning of SD cards with multiple partitions, ideal for developers or advanced users in scenarios like server Raspberry Pi deployments or forensic drone data copies. It’s free, exact, and handles any file system, but demands caution to avoid wiping the wrong drive. Use it when GUI tools fall short, like cloning to mismatched sizes after manual prep. In 2025, it’s still a staple for Linux enthusiasts cloning MiSTer cards via terminals. Pair with pv for progress bars.
Advantages:
- Free and built-in on Linux/Mac
- Precise, retains all data including hidden partitions
- Customizable with block sizes for speed
- Cross-platform via terminals
- No extra software needed
Disadvantages:
- High risk of data loss if devices misidentified
- No GUI, steep learning curve
- Slow without optimizations
- No automatic resizing
- Requires unmounting partitions first
Step 1: Identify Your Devices
Open a terminal and run lsblk (Linux) or diskutil list (macOS) to locate your source and target SD cards.
- The source is the SD card you want to clone (e.g., /dev/sdX or /dev/rdiskX)
- The target is the SD card you’re writing to (e.g., /dev/sdY or /dev/rdiskY)
Make sure to unmount all partitions on both cards before proceeding to avoid data corruption.
Step 2: Run the dd Command
Use the following command to start the cloning process:
sudo dd if=/dev/sdX of=/dev/sdY bs=4M conv=notrunc,noerror status=progress
Here’s what each part means:
- sudo — runs the command with administrative privileges
- dd — the disk duplication tool
- if=/dev/sdX — input file (your source SD card)
- of=/dev/sdY — output file (your target SD card)
- bs=4M — sets the block size to 4 megabytes for faster copying
- conv=notrunc,noerror —
- notrunc prevents truncating the output
- noerror tells dd to continue even if it encounters read errors
- status=progress — shows real-time progress during the copy
Double-check your device paths before running this command. A mistake here can overwrite the wrong disk.
Step 3: Finalize and Eject
Once the copy is complete, run:
sync
This ensures all data is written to the target card. Then safely eject both SD cards.
How to make full use of the remaining space
dd doesn’t support resizing partitions when cloning an SD card. To manage any leftover space after cloning to a larger card, you’ll need to use your system’s built-in tools gparted or fdisk. These utilities let you expand existing partitions or create new ones to fully utilize the extra space.
If you prefer a safer, menu-driven alternative to dd, Clonezilla is a great choice. It supports multi-partition cloning, works across file systems, and offers compression and recovery options—all through a guided interface. Let’s explore how Clonezilla simplifies advanced SD card cloning.
🖥️ OS: System Independent (a Bootable CD/USB)
⚙️ Functions: ✅ Full disk cloning, ✅ Partition-specific cloning, ✅ Image creation and restoration, ✅ System migration
Clonezilla is a free, bootable Linux-based utility designed for full-disk cloning, including SD cards with multiple partitions. It’s especially useful for IT professionals handling complex tasks such as bulk Android device preparation or recovering SD cards with partitions that Windows cannot recognize.
Running entirely from a USB drive, Clonezilla operates independently of your operating system and offers built-in compression and verification to ensure efficient, reliable results. Its support for multiple file systems makes it a versatile choice, and by 2025, the server edition has become a go-to solution for batch deployments.
Advantages:
- Free and open-source
- Works offline via Live USB
- Compresses images to save space
- Verifies clones thoroughly
- Supports massive deployments
Disadvantages:
- Requires creating bootable media
- Menu-based, not fully GUI
- Time-consuming setup
- Overkill for simple tasks
- Needs tech knowledge for options
Step 1: Prepare the Clonezilla USB
Download the latest Clonezilla ISO from the official site. Use a tool like Rufus or balenaEtcher to create a bootable USB drive.
Plug it in and set your computer to boot from USB in the BIOS/UEFI menu.
Step 2: Launch Clonezilla and Start Cloning
Boot into Clonezilla live.
choose the device-to-device option.
Select your source SD card (the one you’re copying) and your target SD card (the one you’re writing to).
Review the partition details, confirm they’re correct, and follow the guided prompts.
Step 3: Complete the Process
Clonezilla will copy the entire card, including all partitions. Wait for the process to finish, then choose reboot or power off.
Clonezilla rounds out the advanced options we’ve covered. Whether you prefer the precision of dd or the guided flexibility of Clonezilla, the right choice depends on your workflow and comfort level with command-line versus menu-driven tools.
Renee Becca – Safe and Quick System Migration to SSD
Automatic 4K alignment Improves SSD performance during system migration.
Support GPT and MBR Automatically adapt to the suitable partition format.
Support NTFS and FAT32 Redeploy various files in different file systems.
Back up quickly Back up files at up to 3,000MB/min.
Overall backup schedule Support system redeployment/system backup/partition backup/disk backup/disk clone.
Automatic 4K alignment Improve SSD performance
Support GPT and MBR Intelligently adapt to a partition format
Support NTFS and FAT32 Redeploy files in different file systems
Cloning an SD card with multiple partitions is essential for safeguarding data or switching to new storage in devices like Raspberry Pi or cameras. Renee Becca emerges as the standout tool with its intuitive design, multi-partition support, speedy process, and reliability. Download it today—you’ll see why it’s a game-changer for hassle-free clones.
Can SD cards have multiple partitions?
Yes, SD cards can be divided into two or more partitions. You can create multiple partitions on an SD card using tools like Disk Management in Windows or Disk Utility in macOS. By dividing the SD card into multiple partitions, you can allocate storage space for different purposes or operating systems on the same SD card.
Can you clone a drive with multiple partitions?
Of course, you can clone a drive with multiple partitions. Cloning software like Clonezilla and Renee Becca allows you to clone all partitions from one drive to another, creating an exact copy of the original drive with all partitions intact. This can be useful for backing up or migrating data to a new drive.
Why isn't my cloned SD card booting properly after cloning?
If your cloned SD card isn’t booting, it could be due to mismatched partition tables or boot sectors not transferring correctly—common with embedded devices like Raspberry Pi. First, verify the clone using tools like Clonezilla’s verification mode or Check “Copy all Sectors” in Renee Becca. Ensure the target card is the same or larger size, and try reseating it in the device.
Can I clone an SD card with multiple partitions to a much larger one without wasting space?
Absolutely, but you’ll need software that resizes partitions automatically. Tools like Renee Becca or SD Card Copier let you expand partitions during the clone to utilize the extra space. For instance, cloning a 32GB Raspberry Pi card to 128GB will leave unallocated space unless adjusted—drag boundaries in the software to fill it, ensuring your root partition grows for more storage.
What should I do if Windows only recognizes one partition on my multi-partition SD card?
This happens because Windows might not support non-NTFS/FAT formats like ext4. Use a card reader and tools like Renee Becca or Win32 Disk Imager, which clone the whole device, not just visible partitions. Avoid Explorer copies; instead, image the raw device. If needed, boot into Linux for better visibility during prep.
Is it safe to clone an SD card while it's in use on my device?
No, cloning a live SD card risks data corruption from ongoing writes. Always remove it from the device (e.g., power off your drone or Switch), insert into a reader on your PC, and clone offline. For minimal downtime, use quick tools like dd with progress monitoring to speed things up.
How can I verify that all partitions cloned correctly without testing in the device?
After cloning, use verification features in software like Balena Etcher or Clonezilla, which compare hashes. Alternatively, mount the cloned card on a PC (use Linux for full partition access) and check file integrity with commands like diff or tools like Beyond Compare. This catches errors early, especially for critical data like camera RAW files.
What if my target SD card is from a different brand—will cloning still work?
Yes, cloning is brand-agnostic as long as capacities match or the target is larger. Differences in speed or endurance might affect performance post-clone, but data transfers fine. Test with a small card first; for example, cloning a SanDisk to a Samsung for Android use works seamlessly with Renee Becca.
Can I clone only specific partitions from an SD card with multiple ones?
Definitely—many tools support selective cloning. In Renee Becca, choose “Partition Clone” instead of full disk. This is useful for isolating data partitions from boot ones, like grabbing just game saves from a Nintendo Switch card without the system files.
Renee Becca – Safe and Quick System Migration to SSD
Automatic 4K alignment Improves SSD performance during system migration.
Support GPT and MBR Automatically adapt to the suitable partition format.
Support NTFS and FAT32 Redeploy various files in different file systems.
Back up quickly Back up files at up to 3,000MB/min.
Overall backup schedule Support system redeployment/system backup/partition backup/disk backup/disk clone.
Automatic 4K alignment Improve SSD performance
Support GPT and MBR Intelligently adapt to a partition format
Support NTFS and FAT32 Redeploy files in different file systems
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