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ProTools and Apollo Interfaces: How to make UA’s Matrix I/O and PT’s I/O Play Nice!

My favorite musician quote is by Jeff Buckly, “There’s music… and thene there’s waiting to make music.” When the gear fails us or is problematic it can be incredibly frustrating and time consuming.

The latest in universal Audio’s Interfaces are the latest in the X series converters. D/a Conversions sparkle and stand out that much more than before! I feel like this is the first time we can finally hear what the commercial studio converters like Prism and Burhl are sonicaly offering.

Arguably, one of the toughest things about setting up multiple Apollo’s is the Matrix I/O. The key is that all the channels match in here and again in ProTools, together! Syncing the proprietary UA Console Software’s “Matrix I/O” to ProTools “I/O settings” might seem difficult so I’ve cracked the simple code and laid it out for you here. Start by first daisy changing your Apollos together via thunderbolt. Thunderbolt 2 and 3 issues can be resolved with a TB2->TB3 dongle successfully.

This info is very hard to find online so I consolidated it all for those in need.

This blog post is also a place for others to add other helpful tips for users like me in the comments below! I hope it helps.

Leave a comment below if it did or if you have additional suggestions! There’s certainly more than one way to do this.


Computer first, Primary Apollo next, (Main Apollo reads, “INT, which means the internal clock source and is the one the whole session is running off of this one. Primary should be the highest model converters so X series. All other Apollos follow. Next fire up the final Apollo (Twin or Twin X, as a remote or whatever other Apollos you have). Then you can turn on software. Turn on UA’s Console software first, double check sample rate (make sure when session loads, they are both in sync with bit depth and sample rate. If they’re off, update both programs or try a fresh re-install. That works 75% of the time). Turning on in this order ensures External remote syncs properly and they won’t get stuck, as they occasionally do (truust me), on the wrong clock source.


The key is that until you have Console software I/O Matrix set correctly (see screenshot), PT will “default” PT I/O all wrong and you’ll be pulling your hair out. The other key is that channel numbers are what need to match up in the Console’s “I/O Matrix” with your protools I/O channel numbers. The last key to the puzzle is Pt only allows 32 channels (unless you have Elite HD version) and I’ve got too ins and outs with just a twin and a 16 so I needed to pair things down in Console.

I have spent almost 2 decades perfecting and curating what I think is the perfect way to sync multiple interface gear and label your I/O intuitively for your recording studio. My setup is a new UA Apollo X16 (on Thunderbolt 3) with a XTwin which is used only for monitor control, TB and the two sets of alt Monitors as a remote. Tens of thousands of other studio owners use this popular setup but getting the Matrix I/O in UA’s Console software to play nice with ProTools I/O is a hat trick in itself!

You’ll need to start in Console FIRST.


Check out the Console I/O setup in the screenshot below. The idea is to have that I/O match PT exactly. You can have up to three monitor sets with the x16. The first will go out the regular XLR outs of the X16 on the rear. The second, as the manual says, MUST go out 1-2 (accessed with the ALT button on the Twin) and the third is forced on to Line Outs 3-4 (which you access with the FCN button on the Twin). * UA Rep said he wishes this was assignable, alas it is not.

PRO TIP 1: Something that kept tripping me up: When powering up your strudio for a work session, make sure you turn on the master clock unit FIRST, and THEN the remote (external sync) module. Other users report issues with them getting locked out of EXT and switching to INT if turned off in wrong order! They can get stuck there and think both or the wrong unit is master (INT cloick source). This can cause buzzing and strange noises.

PRO TIP 2: Also make sure the hierarchy in Console software “Hardware” settings are correct. Mine weren’t and I couldn’t figure out why monitors wouldn’t play sound at first! Turns out it was because The Twin was “On Top” and was clock source, therefore monitor outs were from Twin and system ignored the x16 monitor outs. Put the x16 (with the better converters) as clock source and “on top” in console hardware settings. Turn him on first and off last!

On older macs you needed to have Apollo units on before mac, this isn’t necessary with new units according to UA.

PRO TIP 3: As of 2021 there’s an occasional noise / buzzing glitch in the system that can be fixed by changing the sample rate in the Apollo Console app. If I was running a session at 48k, I’d just change it to 44.1 and then switch back to 48k and this can reset the converters and clear out this glitch and others!

Now with multiple units, Pt only allows 32 channels and you now have got too many so you need to pair things down in Console software (See screenshot of how UA set me up. Works awesome).


Before we set up your new I/O, it was recommended to me to turn off any tracks in the session you have open by selecting “None” for all your ins and outs. This will make sure I/O pulls console I/O cleanly without mistakes from PT.

PRO TIP 1: Hold alt (option) key while clicking “None” to make all tracks none.

Next, open your PT I/O settings from the setup tab. Take a deep breath, you got this. First, hilight and delete all existing I/O by selecting it and deleting (ins, outs, bus, inserts). Click default button on the bottom of this screen once all channels are removed (on each tab up top, ins, out, busses, inserts) and it’ll pull all the above into PT seamlessly! Tada! Next, rename the following and create sub-paths in outputs (ins will create a subpath for you automatically, not outs for some reason). Select the path, it’ll hilight in blue, then click “New Supath. Select 2 Mono channels.

In latest, non-legacy versions of PT you’ss see Outputs can no longer have sub-paths like inputs for some reason. The sub-path button has been removed in later versions of PT for output tab only. Anyway, if you can’t subpath, use this setup of dual mono channels under each stereo pair.

Do you have a different way to run your patchbay and I/O setup? Post your ideas in the comments below.

Remember, Monitor Out of the X16 in Console Matrix I/O is set to 1-2. All channnels must match on both PT and Console right? That’s the key! So therefore:

Line out 1-2 in PT should now be ALT 1 monitor
Line 3-4 should be set to ALT Monitor 2
5-16 are your outputs.

Next rename them accordingly. The x16 will show up as “A” with the letter A in front of all your ins and outs and other units will be “B” and so on. I recommend changing “A” to “X16” and “B” to “Twin” or whatever you have.

Next make a subpath for those without (only outputs I believe), select to have 2 mono paths to do this correctly.

PRO TIP 2: Your headphone cues in console (you have 2) will have their cue source set to “Mix by default. This means the musicians will hear whatever you hear in the control room: the mix. But maybe the drummer doesn’t want to hear digital drum track and others do? You need to make a cue1 send for everyone and a Cue 2 send for him. I recommend setting Cue 1 to “mirror to output” lines 5-6 and send your alternative Cue 1 mixes down that path by inserting a send on the drum track, for insistence, to 5-6 and use that send fader to dial in the right amount. I don’t like using Console too much, most people find it cumbersome too but I do liker this feature.

Lastly, “Export” your settings so you can import them into future sessions if need be!

PRO TIP: When you export PT I?O settings it saves all 6 tabs (ins, outs, inserts, bus, etc) but when you Import, it only imports the tab you’re on so you’ll have to import each tab individually. This is so you can upload just ins, for example and not mess up others.

TURNING OFF SOME CHANNELS: This part was toughest for me at the beginning. Note that in the screenshots of outs and busses I turned off None (6) / None (7)”. This should be done on your rig too. In I/O Matrix 3, 4, 5, 6 outputs are off too because 1-2 is alt monitors and you want the rest of the channel numbers to match and load the same in PT I/O so you’ll have to shuffle them into this order to get hat to happen (screenshot). Cascade mode helped me a lot here, look it up. Inserts 1-2 should be turned off in PT I/O too so they don’t show up in mix/edit window with any of the other turned off channels.

Check out the screenshots for my new I/O Setup, I wish I had these screenshots when I was attempting to slave multiple UA Apollo’s!

Good luck! I really hope these tips help some one else. Post other tips here in this thread that I missed that helped you! Big shoutout to Warren at UA for taking hours with me to take me across the finish line.

Don’t get frustrated with it, you got this ->

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