В том кафе, куда мы часто ходим, чизкейк подают с ягодами.

Том is in the prepositional case because it follows в in a location meaning: in / at that café.

• тот = that
• том = prepositional singular form of тот

So:

• в том кафе = in/at that café

A useful thing to notice: the noun кафе does not change its form, but the pronoun тот still does, so the case is shown by том.

Most Russian nouns do decline, but кафе is one of the common indeclinable nouns. That means its form stays the same in all cases.

So you get:

• это кафе
• в кафе
• из кафе
• к кафе

The noun stays кафе, while other words around it may change:

• в этом кафе
• в том кафе
• из того кафе

This is very common with some borrowed words.

This is a very common question, because English uses where for both ideas.

Russian often distinguishes between:

• где = where, in the sense of location
• куда = where to, in the sense of destination / motion toward

Since ходить means to go (movement), Russian naturally uses куда:

• кафе, куда мы ходим = the café that we go to

If you used где, it would sound more like where we are / where we spend time, not where we go.

So in this sentence, куда matches the verb of motion.

Because ходим means we go regularly / habitually / back and forth, while идём means we are going right now.

Compare:

• мы часто ходим = we often go
• мы идём = we are going
• мы пойдём = we will go

The adverb часто already suggests repetition, so ходим is exactly the right choice. It is the imperfective verb used for repeated or habitual action.

Both relate to going, but they are used differently:

• идти = going in one direction, one specific trip, right now or in a concrete instance
• ходить = going habitually, repeatedly, or in various directions

In this sentence:

• куда мы часто ходим = where we often go

That repeated idea requires ходить, not идти.

Because куда мы часто ходим is a relative clause inserted into the main sentence.

Main sentence:

• В том кафе чизкейк подают с ягодами.

Inserted descriptive clause:

• куда мы часто ходим

So the full sentence becomes:

• В том кафе, куда мы часто ходим, чизкейк подают с ягодами.

In English, this is similar to:

• In that café, which we often go to, they serve cheesecake with berries.

The commas show that this middle part is additional information about кафе.

Russian often uses the 3rd person plural with no stated subject to mean something like:

• they serve
• people serve
• it is served

So чизкейк подают с ягодами literally means:

• They serve cheesecake with berries

But in natural English, we often translate it more impersonally:

• The cheesecake is served with berries
• They serve cheesecake with berries

This is a very normal Russian way to talk about what is generally done in restaurants, cafés, stores, etc.

Here чизкейк is the direct object of подают, so it should be in the accusative case.

But чизкейк is:

• masculine
• singular
• inanimate

For inanimate masculine singular nouns, the accusative form is the same as the nominative form.

So:

• nominative: чизкейк
• accusative: чизкейк

That is why the form does not change.

If it were animate, the accusative would often look like the genitive instead.

Ягодами is in the instrumental case because after с meaning with (accompaniment), Russian normally uses the instrumental.

So:

• ягоды = berries
• с ягодами = with berries

This structure is extremely common:

• чай с лимоном = tea with lemon
• кофе с молоком = coffee with milk
• блины с ягодами = pancakes with berries

Here it means the cheesecake is served with berries, either alongside them or topped with them, depending on context.

It can correspond to either in or at in English, depending on what sounds natural in the situation.

Russian uses в here because it is talking about being in that place / at that establishment. In English, we often prefer at that café when speaking generally about a business, but in that café is also possible if we are emphasizing the physical interior.

So the Russian phrase is broad enough to cover both.

Yes. Russian word order is more flexible than English word order. This sentence is natural as written, but other orders are possible depending on emphasis.

For example:

• В том кафе, куда мы часто ходим, чизкейк подают с ягодами.
• Чизкейк в том кафе, куда мы часто ходим, подают с ягодами.

The basic meaning stays the same, but the focus changes slightly. The original version starts by setting the scene: in that café...

That is a very natural way to introduce a sentence like this in Russian.

Literally, it is closer to where we often go. But in English, the most natural translation may be:

• the café we often go to
• the café that we often go to

Russian does not need a preposition at the end the way English often does. The idea of movement toward the place is already built into куда.

So:

• кафе, куда мы часто ходим
  means
• the café where we often go
• the café we often go to

Both are good English equivalents.