How to set custom connection properties on DataSource in Spring Boot 1.3.x with default Tomcat connection pool

Setting the pools connectionProperties should work. Those will be passed to the JDBC driver. Add this to application.properties:

spring.datasource.connectionProperties: defaultRowPrefetch=1000;defaultBatchValue=1000

Edit (some background information):

Note also that you can configure any of the DataSource implementation specific properties via spring.datasource.*: refer to the documentation of the connection pool implementation you are using for more details.

source: spring-boot documentation

Some additional information to complement the answer by @Cyril. If you want to upvote use his answer, not mine.

I was a little bit puzzled how easy it is to set additional connection properties that in the end get used while creating the database connection. So I did a little bit of research.

spring.datasource.connectionProperties is not mentioned in the reference. I created an issue because of this. If I had used the Spring Boot YML editor, I would have seen which properties are supported. Here is what STS suggests when you create an application.yml and hit Ctrl+Space:

The dash does not matter because of relaxed binding but if you interpret it literally the propertys name is spring.datasource.connection-properties.

The correct setup in application.yml looks like this:

spring:
    datasource:
        connection-properties: defaultBatchValue=1000;defaultRowPrefetch=1000
        ...

This gets honored which is proven by my perf4j measurements of mass SELECTs.

Before:

2016-01-19 08:58:32.604 INFO 15108 --- [ main] org.perf4j.TimingLogger : start[1453190311227] time[1377] tag[get elements]

After:

2016-01-19 08:09:18.214 INFO 9152 --- [ main] org.perf4j.TimingLogger : start[1453187358066] time[147] tag[get elements]

The time taken to complete the SQL statement drops from 1377ms to 147, which is an enormous gain in performance.

As Spring Boot is EOL for a long time I switched to Spring Boot 2.1 with its new default connection pool Hikari. Here the solution is even more simply and can be done in the application.properties or (like shown here) application.yml:

spring:
  datasource:
    hikari:
      data-source-properties:
        defaultRowPrefetch: 1000

(In a real-life config there would be several other configuration items but as they are not of interest for the question asked I simply left them out in my example)