Two separate windows are opened using the gaston(), plotlyjs() or inspectdr() backends.
See also one solution here using Plots.jl’ pyplot() backend, this one requiring the keyword reuse=false. Copied it below for convenience:
using Plots; pyplot()
x = 1:0.1:100
y1, y2 = sin.(x), cos.(x)
p1 = plot(x,y1)
p2 = plot(x,y2, reuse=false)