Learn Hardcore Portuguese (Brazil): Embora todos estejam ocupados, a chefe quer que cada funcionário faça uma pausa. - Although everyone is busy, the boss wants each employee to take a break.

embora todos estejam ocupados
Embora (although / even though) is a conjunction that almost always requires the present subjunctive when it introduces something that contrasts with the main idea.
a chefe quer que cada funcionário faça uma pausa
After quer que (wants that / wants [someone] to), Portuguese uses the subjunctive for the verb in the subordinate clause (faça).

So:

estão → present indicative
estejam → present subjunctive
faz → present indicative
faça → present subjunctive

The sentence combines two classic subjunctive triggers:
embora + subjunctive, and quer que + subjunctive.

How are estejam and faça formed from estar and fazer?

They’re the present subjunctive forms:

From estar:
- eu esteja
- você / ele / ela esteja
- nós estejamos
- vocês / eles / elas estejam ← used in the sentence
From fazer:
- eu faça
- você / ele / ela faça
- nós façamos
- vocês / eles / elas façam

In the sentence:

todos estejam → todos is plural, so estejam (they).
cada funcionário faça → cada funcionário is grammatically singular, so faça (he/she).

Is embora always followed by the subjunctive?

When embora means although / even though, yes, it normally takes the subjunctive:

Embora esteja cansado, vou trabalhar.
(Although I’m tired, I’ll work.)
Embora todos estejam ocupados, ...

In modern Brazilian Portuguese, using the indicative after embora in this meaning sounds odd or non‑standard in most contexts.

Be careful: embora can also mean away / off in expressions like:

Ele foi embora. (He went away.)

In that case it’s not a conjunction and doesn’t take a verb after it in the same way; it’s just part of a set phrase.

What’s the difference between embora and apesar de (que)?

Both introduce contrast (like although / despite), but they work a bit differently:

embora
- subjunctive
- Embora todos estejam ocupados, a chefe quer...
apesar de
- noun / infinitive
- Apesar do cansaço, a chefe quer...
- Apesar de todos estarem ocupados, a chefe quer...
apesar de que
- subjunctive (more formal)
- Apesar de que todos estejam ocupados, a chefe quer...

So you can rewrite the sentence as:

Apesar de todos estarem ocupados, a chefe quer que cada funcionário faça uma pausa.

Meaning is very similar; embora is shorter and very common in speech.

Why is it a chefe and not o chefe or chefa?

chefe is a gender‑neutral noun; the article shows the gender:
- o chefe = male boss
- a chefe = female boss
chefa does exist in some informal speech, but a chefe is the neutral, more standard form.

So a chefe tells you the boss is female.

Why is it quer que cada funcionário faça and not quer cada funcionário fazer?

Portuguese uses querer que + subjunctive when someone wants another person to do something:

A chefe quer que cada funcionário faça uma pausa.
(The boss wants each employee to take a break.)

If the boss wants to do something herself, you use quer + infinitive:

A chefe quer fazer uma pausa.
(The boss wants to take a break.)

So:

quer fazer → same subject (the boss does the action)
quer que ... faça → different subject (employees do the action)

Why is it cada funcionário faça with a singular verb if we’re talking about multiple employees?

Because cada (each) is grammatically singular in Portuguese, just like in English:

English: Each employee takes a break. (not take)
Portuguese: Cada funcionário faz uma pausa.

So:

cada
- singular noun (funcionário)
and the verb agrees in the singular: faça

Even though we know it’s many people in total, the grammar looks at each one individually.

What’s the difference between todos here and todo mundo?

In this sentence, todos means everyone / all of them:

Embora todos estejam ocupados, ...

You could say:

Embora todo mundo esteja ocupado, ... (very common in speech)
Embora todas as pessoas estejam ocupadas, ... (more explicit, a bit heavier)

Some nuances:

todos can be:
- a pronoun: Todos chegaram. (Everyone arrived.)
- or an adjective: todos os funcionários. (all the employees)
todo mundo is always a pronoun meaning everybody / everyone and is more informal/colloquial.

Here, todos is a nice neutral choice, not overly formal or slangy.

Could we change the word order to put the embora part at the end?

Yes, that’s possible and natural:

A chefe quer que cada funcionário faça uma pausa, embora todos estejam ocupados.

Both orders are fine:

Embora todos estejam ocupados, a chefe quer...
A chefe quer..., embora todos estejam ocupados.

The comma is still needed to separate the main clause from the embora clause.

Is fazer uma pausa the normal way to say take a break?

Yes, fazer uma pausa is a very natural collocation:

faça uma pausa = take a break
Vamos fazer uma pausa. = Let’s take a break.

Other possibilities exist but have slightly different nuances:

fazer um intervalo – often for class, meetings, TV, etc.
fazer uma pausa para o café – take a coffee break
dar uma pausa – used, but often with things (e.g. dar uma pausa no trabalho = pause/stop work for a bit)
descansar – to rest (focus on resting, not specifically “a break”)

In a work context, telling employees to fazer uma pausa is very idiomatic.

How would the sentence change if the boss were male?

You mainly change the article (and any referring adjectives, if present):

Embora todos estejam ocupados, o chefe quer que cada funcionário faça uma pausa.

Changes:

a chefe → o chefe
Everything else stays the same, because:
quer doesn’t change with gender.
faça agrees with cada funcionário, not with the boss.

Is funcionário always masculine? How do I make it inclusive?

funcionário is the masculine form. The basic pair is:

o funcionário – male employee
a funcionária – female employee

In the generic, traditional grammar, the masculine plural can stand for a mixed group:

os funcionários = the employees (men and/or women)

More explicitly inclusive options you might see:

cada funcionário ou funcionária – each male or female employee
cada pessoa funcionária – (more activist / inclusive style)
cada colaborador / cada colaboradora – some companies prefer colaborador(a) instead of funcionário(a).

In your sentence, cada funcionário is grammatically masculine singular and generic unless context specifies otherwise.