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I'm using Kafka Spring to create some listeners for kafka topics. The topics are created automatically when app starts.

That's how a listener looks like:

 @KafkaListener(topics = "${kafka.topics.message.readFormatForMessageFromProfile.in}")

The problem is that i want to increase the number of partitions to 3 and i have no clue how to do that.

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You can use topicPartitions attribute of @KafkaListner annotation.

@KafkaListener(id = "someId", topicPartitions = { @TopicPartition(topic = "${kafka.topics.message.readFormatForMessageFromProfile.in}", partitionOffsets = @PartitionOffset(partition = "0", initialOffset = "0"))})

You can add multiple @TopicPartition

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This doesn't create the partitions, it just tells the consumer which partitions to listen on.
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I'm not an expert of Kafka Spring but I know how it's possible to do that using the official Admin Client API. By the way I see the following in the Kafka Spring documentation :

https://docs.spring.io/spring-kafka/reference/htmlsingle/#_configuring_topics

Reading this note :

If the broker supports it (1.0.0 or higher), the admin will increase the number of partitions if it is found that an existing topic has fewer partitions than the NewTopic.numPartitions.

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