In bibliotheca magistra discipulos libros in scrinio ponere iubet.

Because the two in phrases are doing the same basic job—showing place—but with different nouns:

• in bibliotheca = in the library
• in scrinio = in/on the bookcase, cabinet, desk, or chest depending on context

In both phrases, in is followed by the ablative case, which usually shows location: where something happens.

A useful rule:

• in + ablative = in/on somewhere, at rest
• in + accusative = into/onto somewhere, motion toward

Here both are ablative, so both mean location, not motion into.

Because after in meaning in or inside, Latin normally uses the ablative to show location.

So:

• nominative: bibliotheca = the library as a subject
• ablative: in bibliotheca = in the library

This is a first-declension noun, and the ablative singular ending is -ā. In many textbooks it is written without the long mark, so you see bibliotheca, but it is understood as ablative here because of the preposition in.

Because scrinium is a second-declension neuter noun, and after in meaning location it must be in the ablative singular:

• nominative/accusative singular: scrinium
• ablative singular: scriniō (often written scrinio)

So in scrinio means in the cabinet / desk / chest / bookcase.

Magistra is nominative singular because it is the subject of the main verb iubet.

The basic structure is:

• magistra = the teacher
• iubet = orders

So the teacher orders...

Even though Latin word order is flexible, the subject is still recognized by its case ending, not just by position.

They are both accusative, but for different reasons.

• discipulos is the person being ordered
• libros is the thing being put

With iubet (orders), Latin often uses this pattern:

• person in the accusative
• infinitive
• and then any object of that infinitive

So here:

• magistra discipulos ... ponere iubet = the teacher orders the students to put...

And within the infinitive phrase:

• libros ponere = to put the books

So:

• discipulos = accusative subject of ponere
• libros = direct object of ponere

Because after iubere (to order), Latin commonly uses an infinitive construction rather than a clause with that or to in the English way.

So Latin says, literally:

• the teacher orders the students the books to put

But in natural English we say:

• the teacher orders the students to put the books...

This is a very common Latin pattern:

• iubeo + accusative person + infinitive

Example:

• magister puerum venire iubet = the teacher orders the boy to come

Because iubeo does not usually take the person ordered in the dative. It takes the person in the accusative.

So Latin says:

• discipulos iubet = she orders the students

not:

• discipulis iubet

This is worth memorizing as a pattern:

• iubeo aliquem aliquid facere = I order someone to do something

Some other Latin verbs of ordering use different constructions, so this is specific and important.

A good way to break it up is:

• In bibliotheca = in the library
• magistra = the teacher
• discipulos = the students
• libros = the books
• in scrinio = in the cabinet / bookcase / desk
• ponere = to put
• iubet = orders

Main verb:

• magistra ... iubet = the teacher orders

What she orders:

• discipulos libros in scrinio ponere = the students to put the books in the scrinium

So the full structure is:

• [location] + [subject] + [person ordered] + [object] + [place of infinitive action] + [infinitive] + [main verb]

Most naturally, it sets the scene for the main action:

• In bibliotheca magistra ... iubet = In the library, the teacher orders...

So it tells us where the ordering happens.

Meanwhile:

• in scrinio goes with ponere = to put ... in the cabinet/bookcase/etc.

So the sentence has two place phrases with different functions:

• in bibliotheca = where the teacher is giving the order
• in scrinio = where the books are to be put

It may feel unusual from an English perspective, but it is normal for Latin.

English strongly depends on word order:

• The teacher orders the students to put the books...

Latin depends much more on case endings, so the order can be flexible.

This sentence places the main verb iubet at the end, which is very common in Latin prose.

A Latin reader can tell the roles from the forms:

• magistra = nominative subject
• discipulos = accusative
• libros = accusative
• ponere = infinitive
• iubet = main verb

So even if the order changes, the meaning can remain the same.

Yes, to a large extent.

For example, Latin could also say things like:

• Magistra in bibliotheca discipulos libros in scrinio ponere iubet.
• Discipulos magistra in bibliotheca libros in scrinio ponere iubet.

These still mean essentially the same thing, because the case endings show who is doing what.

However, different word orders can change emphasis. For example:

• putting in bibliotheca first emphasizes the setting
• putting discipulos early may emphasize the students

So the order is flexible, but not meaningless.

Because libros is the accusative plural of liber (book).

Forms:

• nominative singular: liber
• accusative singular: librum
• nominative plural: libri
• accusative plural: libros

Since ponere needs an object, libros here means the books.

In a sense, it is both.

More exactly:

• with the main verb iubet, discipulos is the person ordered
• within the infinitive phrase, discipulos is the understood subject of ponere

So the students are the ones who are supposed to put the books.

This is a standard Latin construction often called an accusative + infinitive-type pattern after certain verbs, though with iubeo it is specifically the normal command structure.

Because ponere is already an infinitive, and the infinitive itself expresses the idea that English often shows with to.

So:

• ponere = to put

Latin does not need a separate word for to here. The verb form itself carries that meaning.

A scrinium is not necessarily a modern “desk” in the narrow sense. Depending on context, it can mean something like:

• a box or chest
• a case for books or documents
• a cabinet
• a book-storage container
• sometimes a desk-like piece of furniture

So in scrinio means the books are being put into some kind of storage place or container for books/documents. The exact English word depends on context.

Because after iubeo, Latin normally prefers the simpler construction:

• iubeo + accusative person + infinitive

So:

• magistra discipulos ponere iubet

rather than a clause with ut.

Other verbs of ordering or persuading may use different constructions, but iubeo very commonly takes the infinitive pattern seen here.