Were EC2 and RDS originally running in the same subnet?
Looking at the configuration diagram, the subnets are separated and communication occurs between AZs.
Communication between AZs will result in a difference in performance compared to communication within the same AZ.
You can perform a simple benchmark test by following the steps in the document below, which may be helpful.
Additionally, IO performance may be improved somewhat by changing the RDS storage settings.
@Riku_Kobayashi So the first infrastructure was all in one subdomain. I tried to move the new one to one Azs to eu-cental-1b but it didn't help. There are still EC2 and rds in different subdomains. Can the fact that they are in private networks and EC2 uses a NAT gateway to communicate with the Internet have an impact on latency?