Use conditionals to select which output(s) to use. Presumably there is some field (perhaps [@metadata][beat] that's unique for Beats-generated events.
output {
if [@metadata][beat] {
elasticsearch {
hosts => ["http://localhost:9200"]
index => "%{[@metadata][beat]}-%{+YYYY.MM.dd}"
document_type => "%{[@metadata][type]}"
}
} else {
# non-Beats outputs
}
}