Since you are using subplots to plot the data you can use link axis to link the desired axis. Here's the link that explains in more detail. https://www.mathworks.com/help/matlab/ref/linkaxes.html
Or you can manually set the Ylimits for instance in your plot
figure;
subplot(1,2,1)
plot(f_b, P1_b)
title('FFT for baseline')
xlabel('Frequency')
ylabel('|P1(f)|')
subplot(1,2,2)
plot(f_e, P1_e)
% Add a line here to set the y limits
ylim([minimumvalue maximumvalue]) % specify the minimum and maximum value so that both the y axis have the same scale
title('FFT for experimental condition')
xlabel('Frequency')
ylabel('|P1(f)|')