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The alchemist's Mutagen class feature says:

At 1st level, an alchemist discovers how to create a mutagen that he can imbibe in order to heighten his physical prowess at the cost of his personality. It takes 1 hour to brew a dose of mutagen, and once brewed, it remains potent until used. An alchemist can only maintain one dose of mutagen at a time—if he brews a second dose, any existing mutagen becomes inert. As with an extract or bomb, a mutagen that is not in an alchemist’s possession becomes inert until an alchemist picks it up again.

...

A non-alchemist who drinks a mutagen must make a Fortitude save (DC 10 + 1/2 the alchemist’s level + the alchemist’s Intelligence modifier) or become nauseated for 1 hour—a non-alchemist can never gain the benefit of a mutagen, but an alchemist can gain the effects of another alchemist’s mutagen if he drinks it. (Although if the other alchemist creates a different mutagen, the effects of the “stolen” mutagen immediately cease.) The effects of a mutagen do not stack. Whenever an alchemist drinks a mutagen, the effects of any previous mutagen immediately end.

If I'm currently under the effect of a mutagen, and I brew another one, what happens?

Do I lose the effects of the current mutagen, or does it still apply?

The closest thing I can think of is a spellcaster preparing an extended Mage Armor that last for a day or so, and you would keep the effects of it when you prepare another spell in that slot.

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Creating a mutagen does not cancel it's effects

As confirmed by James Jacobs (Creative Director), you may have multiple mutagens in your character, just not active at the same time, as the effects of the old mutagen cease once you drink a new mutagen:

If he's under the effect of a mutagen and starts to brew a second, does the first mutagen immediately end when he starts making the second mutagen? Or does it only end when he's done making the mutagen? Was the time to create the mutagen meant interact with Swift Alchemy at all?

The effects of a mutagen only go away once you drink a new mutagen. It's not something that can be shortened by Swift Alchemy.

If you want, you can use the ability multiple times a day, you just need to take an hour to switch things out.

Also look at the Infused Metagen discovery

When the alchemist creates a mutagen he can infuse it with an extra bit of his own magical power. This inflicts 2 points of Intelligence damage to the alchemist and costs 1,000 gp in rare reagents, but the mutagen created persists on its own and is not rendered inert if the alchemist creates another mutagen. This allows an alchemist to create different types of mutagens and keep them handy for emergencies. This does not allow an alchemist to gain the effects of multiple mutagens—only the most recently imbibed mutagen has any effect.

This discovery allows you to create a mutagen that does not follow the rule of "there must be only one" mutagen. As such, you may brew an infused mutagen while still under the effects of another mutagen without problems, you simply cannot have the benefits of two mutagens at once, at all.

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  • \$\begingroup\$ I'm not sure the discussion of the discovery infused mutagen is helping your answer. Jacobs's quotation address the asker's situation completely, yes? \$\endgroup\$ – Hey I Can Chan Jan 28 at 11:05
  • \$\begingroup\$ Ok, since James Jacobs is the final authority on these type questions, I'm removing my own answer as to not confuse readers. \$\endgroup\$ – Draco-S Jan 28 at 11:08
  • \$\begingroup\$ @HeyICanChan it is merely an extra information that is usually overlooked as I noticed on my searches while answering this question. \$\endgroup\$ – ShadowKras Jan 28 at 11:12
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The old mutagen remains in effect until you drink the new one.

It seems the uncertainty here is what this statement:

if he brews a second dose, any existing mutagen becomes inert.

means by "existing mutagen". Does it mean an existing dose of prepared mutagen, or a dose that you've already consumed?

I think it's the first one, for two reasons. First, if it means a dose of mutagen that you've already consumed, this would allow you to prepare any number of doses of mutagen and carry them all around, so long as you don't do it while under the effect of a previous dose. This is inconsistent with how bombs and extracts both work, which is a strict limit on how many you can have prepared at any time.

Second, and more important, is context. The first paragraph says that the mutagen "remains potent until used". This must refer to a dose of brewed mutagen, because that's the stuff that hasn't been used yet. Immediately after that is the statement that "if he brews a second dose, any existing mutagen becomes inert". And after that, we're told what happens to a dose of mutagen that leaves the alchemist's possession--it also "becomes inert".

So either the writer started out talking about vials of prepared mutagen, then abruptly changed the subject for one sentence, and then changed it back, or else all three sentences are referring to prepared mutagen.

This ends up being nicely symmetric: brewing a dose wipes out the dose you previously brewed, and drinking a dose ends the effect of the dose you previously drank.

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