ISO to MKV: The Ultimate Guide to Remux vs Re-encode for You

 

 

You don't have to choose between "remux" and "re-encode" or bounce between dofferent software when you decide converting ISO to MKV. For Remux, quality is the same on DVDFab and MakeMKV; choose DVDFab as the steadier default (reliable decryption, easy batching) and keep MakeMKV for clean discs. For Re-encode, use H.265 to keep 4K HDR under ~20 GB; DVDFab is faster and simpler with GPU, HandBrake is slower to set up and encode, and VLC is best for quick one-offs.

What do you actually need?

Do you need a 1:1 "digital disc" copy (Remux) that keeps everything intact, or a space-saving, high-quality compressed version (Re-encode) that takes up less storage but still looks great?

❗Here's the problem: most free tools only do one thing, such as MakeMKV for "remux" and HandBrake for "reencode", but none handle encrypted discs properly.

This guide shows you a simple ISO to MKV workflow that removes encryption and lets you choose Remux for 1:1 or Re-encode to save space for each title. We also recommended multi-functional software that you don't have to pick between remux and re-encode.

ISO to MKV Workflow A: The "Lossless Collector" Remux (Passthrough)

📌MKV.Passthrough (Without Quality Loss) — remux the original video, audio, and subtitle streams into an MKV container without re-encoding, preserving source quality and multi-channel audio (e.g., AC3/DTS). This is ideal for home theater playback. 

📌Other MKV Profiles — create compressed MKV files such as H.264/H.265, 3D, or high-resolution profiles when you want smaller sizes or specific playback needs.

🎯Best for: home theaters, 7.1 receivers, and Plex/Jellyfin users who want the original look and sound.

1. Convert Any ISO to MKV with DVDFab DVD Ripper

DVD Ripping Software

DVD Ripper and Blu-ray Ripper allow users to rip the contents of any ISO file, folder, or DVD/Blu-ray disc and convert them to MKV or other digital formats.

 

Tutorial: How to Rip ISO to "MKV Passthrough" with DVDFab DVD Ripper?

You can watch the video or follow the steps:

Step 1: Launch DVDFab 13 and add ISO file

Download DVDFab 13, and select the Ripper module to get started. Insert the disc you want to rip into your optical drive or use the navigation buttons to add an ISO file or folder.

Step 2: Choose output profile

Go to the Profile Switcher to choose "MKV. Passthrough". If you want to convert ISO or DVD to MP4, AVI or MOV, choose others based on your needs.

Optional: Customize output video 

Click "Advanced Settings" and "Video Edit" to customiaze your videos. The first menu will let you modify things like video quality, frame rate, resolution, encoding method, and more.

Meanwhile, the Video Edit menu contains tools that let you crop and trim the video or add subtitles and watermarks.

Other options like picking audio tracks and selecting specific chapters or titles are found on the main menu. 

✅Recommended MKV Settings

Step 3: Start to convert ISO to MKV file

Decide where to save the file by using the menu at the bottom. 

2. Convert ISO to MKV For Free via MakeMKV (Remux)

MakeMKV is a DVD ISO to MKV converter that turns DVD/Blu-ray (including ISO images) into MKV by remuxing the original video, audio, chapters, and subtitles—without re-encoding. That means you retain source quality and structure in an MKV container, ideal for lossless backups and home-theater playback.

Tutorial: How to Convert ISO to MKV free with MakeMKV?

Step 1: Downloaad this free ISO converter on your Windows or Mac PC. Once it is downloaded, proceed to install and launch the software. （The latest version is 1.18.1)

Step 2: Navigate to the "File" tab and select "Open files".

Step 3: Choose the desired video and audio tracks you want to include in the MKV file.

Step 4: Set the output folder where you want the converted MKV file to be saved. Then click on the "Make MKV" button to start the conversion process.

Why DVDFab is the Better Choice for Remux

DVDFab offers more dependable decryption. Its built-in engine usually unlocks protected ISOs and discs that MakeMKV can't handle.

DVDFab's workflow is cleaner and faster. You get a native MKV Passthrough profile, a task queue for batching, and a straightforward interface for multi-title jobs.

DVDFab is more stable. Activation is stable, while MakeMKV relies on beta keys that can lapse.

ISO to MKV Workflow B: The "Space Saver" Re-Encode

Re-encoding converts the original video to a new codec and bitrate to cut size. The target here is simple: use H.265 (HEVC) to fit a 4K HDR movie under ~20 GB while keeping it watchable on TVs, tablets, and phones.

🎯Best for: people who watch on iPad/phone, or anyone with limited NAS space.

1. Convert ISO to MKV with DVDFab (re-encode)

DVDFab DVD Ripper can also decrypt discs/ISOs and re-encode to MKV in one-flow. For re-encoding, it supports H.264 and H.265 with hardware acceleration (NVENC/AMF/QSV), CRF and bitrate targets, audio passthrough or re-encode, and subtitle copy or burn-in.

Tutorial: How to Convert ISO to MKV with DVDFab (Re-Encode)?

Step 1: Open DVDFab DVD Ripper.

Step 2: Choose MKV (H.264 or H.265).

H.265 (HEVC) offers better compression, reducing file size by about 30-50% while maintaining similar quality, making it ideal for 4K HDR and large files. H.264 (AVC) is more widely compatible with older devices but results in larger file sizes for the same quality.

• Use H.265 for 4K or when you need to save space without losing quality.
• Choose H.264 if you need broader compatibility, especially with older devices.

Step 3: Choose the output and start.

2. Convert ISO to MKV free with Handbrake 

HandBrake is a free, open-source transcoder that converts video sources—including many DVD/Blu-ray ISO images—to MKV. It's ideal when you need to shrink file size or tune quality. HandBrake can usually open ISO files directly.

Tutorial: How to Convert ISO to MKV with Handbrake?

Step 1: Download and install the latest version 1.9.2 of HandBrake from https://handbrake.fr/downloads.php

Step 2: Open the ISO file to be converted after starting HandBrake. You can choose the preferred title and chapter.

Step 3: Choose MKV as the preferred format for conversion under Output Settings. Additionally, you can alter the audio, video, and subtitle settings according to your preferences.

✅Here are optimized settings for converting ISO to MKV using HandBrake, balancing good quality and reasonable file size for most users.

• Video: H.264 (x264) or H.265 (x265); RF 20–22; Framerate = Same as source; Preset = Fast/Very Fast. 
• Audio: Passthrough original AC3/DTS when you want surround; otherwise AAC Stereo for compatibility. 
• Subtitles: For forced/foreign parts, use Foreign Audio Scan or add a track; MKV can pass through multiple VobSub/PGS, and you can optionally burn in one.

Step 4: Click the "Start Encode" button to start the conversion. HandBrake will convert the ISO to MKV file according to the selected specifications.

4. Convert ISO to MKV using VLC Media Player

VLC is a media player with a basic convert feature. It can re-encode to MKV with H.264 or H.265 and is handy for quick, one-off conversions when you don’t need advanced controls or batching. It does not handle decryption and offers limited quality tuning compared to dedicated encoders.

Tutorial: How to Convert ISO to MKV with VLC Media Player?

Step 1: Mount and open the ISO file.

Download VLC 3.0.21; Right-click the ISO file and choose "Mount" (this creates a virtual DVD drive)

Step 2: Open the Disc or File

Click on the "Disc" tab; Select "DVD" and make sure the "Disc device" path points to the mounted ISO (virtual DVD drive).

Optional: Check "No disc menus" to skip menus.

Step 3: Customize the videos

Click "Convert / Save" at the bottom; In the next window; Under settings, choose "Convert"; For Profile, select "Video - H.264 + MP3 (MP4)", then click the wrench icon to set Encapsulation as MKV.

• Under the Video Codec tab, make sure Video is enabled and codec = H.264.
• Under Audio Codec, set codec = MP3 or AAC.

Step 4: Choose Output File and Start the Conversion

Click "Browse" to select the destination and name your file (with .mkv extension).

Why DVDFab is the Better Choice for Re-Encoding?

DVDFab is simple and fast. It can decrypt, re-encode (H.264/H.265), and batch jobs in one place. It also uses your graphics card to speed things up.

HandBrake gives lots of settings, but it cannot decrypt. It often needs extra setup (like libdvdcss) and usually runs on the CPU, so 4K HEVC can be slow.

AVLC Media Player can convert ISO to MKV, but it cannot decrypt,  and it has few quality controls, and no real batch tools.

How to Choose the Best ISO to MKV converter?

After thoroughly testing the top ISO to MKV converters, we've compiled a comparison table to help you choose the best option for your needs. This table highlights key features, speed, output quality, and additional functionalities for each converter.

Top DVD Ripping Software Showdown: Paid vs Free Tools Compared and Tested

 

I ran the tests on Windows 10 x64 with an Intel Core i7-6700, 16 GB of RAM, and an NVIDIA GeForce RTX 4060 Ti (8 GB). My source was 8 Mile (1:50:14, 6.13 GB).

DVDFab DVD Ripper is a fast, flexible choice. You can use passthrough to keep the original video and audio, or re-encode to shrink the file while keeping the picture clean. Hardware acceleration speeds the job, and you still control codec, bitrate, audio, and subtitles. MakeMKV prioritizes speed by skipping re-encoding altogether, which makes it ideal for quick backups—but the tradeoff is massive file sizes due to uncompressed output. HandBrake, while strong in re-encoding efficiency, lacks a true passthrough option for video, which can limit its adaptability depending on the user's needs.

For Remux, DVDFab and MakeMKV produce the same quality, but DVDFab is more stable and easier. For Re-encode, DVDFab is faster and just as good or better in quality than HandBrake at the same file size.

FAQs

Can VLC convert DVD ISO to MKV?

Yes, VLC Media Player can convert ISO to MKV free, but it lacks the customization options, speed, and output quality controls that you'd get from specialized software. Here’s a quick overview of how you can do it with VLC:

1. Launch VLC Media Player on your computer. Go to "Media" > "Open File" and select your ISO file.
2. Click "Media" > "Convert/Save" (or press Ctrl + R).
3. In the "Convert" window, select a profile that uses MKV as the container format. You might need to choose a profile with MP4 and then manually change the container to MKV.
4. Choose where you want to save the output file and give it a name with the .mkv extension.
5. Click "Start" to begin the conversion process.

Conclusion

DVDFab isn't just another "converter"; it's the all-in-one media library solution that excels at both Remux and Re-encode workflows. With its reliable decryption, fast GPU acceleration, and batch processing, DVDFab is a multi-functional tool that can seamlessly handle both tasks, offering a smoother, more efficient experience for users who want both quality and flexibility.