Por si acaso, ya tengo anotado el código de referencia en mi cuaderno.

It means just in case.

It introduces the idea of taking a precaution: the speaker has written down the reference code because it might be needed later.

You will often hear:

• Por si acaso, llévate una chaqueta. = Take a jacket, just in case.
• Lo guardo por si acaso. = I’m keeping it, just in case.

In your sentence, por si acaso sets up the reason for the action.

Because por si acaso is being used as an introductory phrase.

Spanish often separates this kind of opening expression with a comma:

• Por suerte, llegamos a tiempo.
• En realidad, no importa.
• Por si acaso, ya tengo...

The comma helps show a pause and makes the sentence easier to read.

Ya here means something like already.

So ya tengo anotado... suggests:

• the action has been done in advance
• the speaker is prepared
• there is no need to worry because it’s taken care of

Compare:

• Tengo anotado el código. = I have the code written down.
• Ya tengo anotado el código. = I already have the code written down.

That ya gives a stronger feeling of readiness.

Tengo anotado focuses on the current result: the code is now written down and available.

It literally works like I have the code noted down or I’ve got the code written down.

Compare:

• Anoté el código. = I wrote down the code.
  Focus: the action itself.
• Tengo anotado el código. = I have the code written down.
  Focus: the result/state now.

This structure is very common in Spanish:

• Tengo reservada una mesa. = I have a table booked.
• Tengo preparada la maleta. = I have the suitcase ready.
• Tengo guardados los documentos. = I have the documents stored/put away.

Because anotado agrees with el código, which is masculine singular.

In this pattern, the past participle agrees with the direct object:

• el código → anotado
• la dirección → anotada
• los documentos → anotados
• las llaves → anotadas

So:

• Tengo anotado el código
• Tengo anotada la referencia
• Tengo anotados los números

No, not exactly.

Even though it may look a bit like I have written down, this is not the normal Spanish perfect tense.

The normal perfect would be:

• he anotado el código

But tengo anotado el código is a different structure:

• tener
  • object + past participle

It describes a resulting state, not simply a completed action.

So:

• He anotado el código = I have written down the code.
• Tengo anotado el código = I have the code written down.

They are related in meaning, but not the same grammar.

Yes, but the nuance changes.

• He anotado el código focuses on the completed action.
• Tengo anotado el código focuses on the fact that it is now written down and available.

In this sentence, tengo anotado sounds especially natural because the point is preparedness: just in case, I already have it noted down.

For this context, tengo anotado is probably the better choice.

Anotar means to note down, to write down, to make a note of.

It is very close to apuntar, and in many situations they overlap.

Examples:

• Anotar un número
• Apuntar un número

Both can mean to write down a number.

A rough tendency:

• anotar can sound a bit more neutral or formal
• apuntar is very common in everyday speech, especially in Spain

So you might also hear:

• Por si acaso, ya tengo apuntado el código de referencia en mi cuaderno.

That would also sound natural.

Código de referencia means reference code.

The structure noun + de + noun is extremely common in Spanish:

• número de teléfono = phone number
• tarjeta de crédito = credit card
• código de acceso = access code
• código de referencia = reference code

Spanish usually does not put one noun directly before another the way English often does.

So instead of reference code, Spanish normally says código de referencia.

Because the code has been written in the notebook.

Use en for location inside/on a place where something is written:

• en mi cuaderno
• en un papel
• en el móvil
• en una libreta

So:

• Lo tengo anotado en mi cuaderno. = I have it written down in my notebook.

Yes, cuaderno is a very standard word for notebook or exercise book.

Depending on context, Spanish might also use:

• libreta = notebook/notepad
• agenda = diary/planner
• bloc = pad, writing pad

But cuaderno is completely natural here.

In Spain, cuaderno and libreta are both common, though they can suggest slightly different kinds of notebooks depending on the speaker.

It can be omitted in some contexts, but keeping mi is very natural here.

• en mi cuaderno = in my notebook
• en el cuaderno = in the notebook

If you say mi cuaderno, you make it clear that it is your own notebook, which fits the sentence well.

Spanish often uses articles instead of possessives with body parts or very obvious possessions:

• Me duele la cabeza
• Se puso el abrigo

But with personal objects like notebooks, both are possible depending on context. Here, mi cuaderno sounds perfectly normal.

Yes, the sentence can be rearranged, though the original order sounds very natural.

Original:

• Por si acaso, ya tengo anotado el código de referencia en mi cuaderno.

Other possible versions:

• Ya tengo anotado el código de referencia en mi cuaderno, por si acaso.
• El código de referencia ya lo tengo anotado en mi cuaderno, por si acaso.
• Por si acaso, tengo ya anotado el código de referencia en mi cuaderno.

The original order works well because:

1. Por si acaso gives the reason first
2. ya adds the idea of preparedness early
3. the rest gives the information clearly

Yes, it sounds natural and standard in Spain.

Nothing in it is strange or overly formal. It is the kind of sentence a native speaker could easily say in everyday conversation.

A slightly more conversational Spain-style alternative might be:

• Por si acaso, ya tengo apuntado el código de referencia en mi cuaderno.

But your original sentence is absolutely correct and natural.