How to Clone Pi OS from a microSD to an NVMe SSD

Migrating your Raspberry Pi’s root filesystem from a microSD card to an NVMe SSD is one of the most significant performance upgrades you can make. It dramatically improves disk I/O, which in turn enhances overall system responsiveness, application load times, and file transfer speeds.

This guide provides a direct walkthrough for cloning your existing Pi OS setup to an NVMe drive using Klon, a tool I built after running into reliability issues with rpi-clone on modern SSD/NVMe setups.

Prerequisites

• Raspberry Pi 4 or 5.
• An NVMe-compatible HAT or adapter.
• An NVMe SSD installed and recognized by the Pi.

Step 1: Identify the Source and Target Drives

First, ensure your system is up-to-date and the NVMe drive is visible.

sudo apt update && sudo apt upgrade -y

Next, identify the block devices. mmcblk0 is typically the microSD card, and your NVMe will appear as nvme0n1.

lsblk

You should see an output similar to this, clearly distinguishing the source and destination:

NAME        MAJ:MIN RM   SIZE RO TYPE MOUNTPOINTS
mmcblk0     179:0    0  59.5G  0 disk
├─mmcblk0p1 179:1    0   256M  0 part /boot
└─mmcblk0p2 179:2    0  59.2G  0 part /
nvme0n1     259:0    0 931.5G  0 disk

Step 2: Install and Clone the System with Klon

rpi-clone is a great script, but it hasn’t aged well with newer device naming and some modern SSD/NVMe behaviors. Because of that, I created Klon: a Go-based cloning tool inspired by rpi-clone, with an explicit plan/confirm flow and better handling of current Linux disk conventions. Repo: https://github.com/woliveiras/klon

Install Klon (Raspberry Pi OS / Debian)

If you want the simplest path, install a prebuilt release:

sudo apt-get update
sudo apt-get install -y curl tar gzip dpkg

Download and install the binary (example for Raspberry Pi 4/5, usually arm64):

VERSION=vX.Y.Z
ARCH=arm64   # or amd64
curl -L -o klon_${VERSION}_linux_${ARCH}.tar.gz \
  https://github.com/woliveiras/klon/releases/download/${VERSION}/klon_${VERSION}_linux_${ARCH}.tar.gz
sudo tar -C /usr/local/bin -xzvf klon_${VERSION}_linux_${ARCH}.tar.gz klon
klon --version

Clone microSD → NVMe with Klon

Klon always shows you a clone plan first and asks for confirmation before it writes anything to the destination disk. For a brand-new SSD, you typically want an initialize + sync clone and then expand root to fill the disk:

sudo klon -f --expand-root nvme0n1

If you prefer the interactive mode (recommended), just run:

sudo klon

Step 3: Configure the Boot Order

After the clone is complete, you must instruct the Raspberry Pi to boot from the new NVMe drive.

sudo raspi-config

Navigate to Advanced Options > Boot Order and select B2 NVMe/USB Boot.

Step 4: Finalize and Reboot

Exit raspi-config, shut down the system, remove the microSD card, and power it back on. Your Raspberry Pi will now boot from the NVMe SSD.

sudo shutdown now

You can verify that the root filesystem (/) is mounted on the NVMe drive by running lsblk again. The output should now show nvme0n1p2 as the root mountpoint.

Troubleshooting

Mount Failure: “Can’t lookup blockdev”

During the clone, you might encounter a mount failure:

Mounting /dev/nvme0n1p2 on /mnt/clone
mount: /mnt/clone: fsconfig() failed: ... Can't lookup blockdev.
Aborting!

This error typically means the kernel has not yet recognized the new partitions that were just created. You can manually force the kernel to re-read the disk’s partition table.

1. Run partprobe targeting your NVMe disk:

   sudo partprobe /dev/nvme0n1

2. Re-run the Klon command:

   sudo klon -f --expand-root nvme0n1