API latency in EB (Elastic Beanstalk)

Unfortunately, anything would be speculation without data. Do you instrument the latency you have from your service (commonly known as time to first byte)? Do you measure your latency between your application and your database? Do you use the logs to identify the latency between the load balancer the application? Which load balancer are you using? Are you looking at the available metrics there (depending on whether it is CLB or ALB)? The way to get your answer is to instrument all of this, then look at causes.