Yes it is. Here is an example of a plot with different y axis colors:
t = linspace(0,1,1000);
a = sin(2*pi*t);
b = sin(4*pi*t);
fig = figure;
left_color = [1 0 0];
right_color = [0 0 1];
set(fig,'defaultAxesColorOrder',[left_color; right_color]);
yyaxis left
plot(t, a)
yyaxis right
plot(t, b)
