Jianxun's solution did the job for me but broke the y value indicator at the bottom left of the window.
I ended up using FuncFormatter
instead (and also stripped the uneccessary trailing zeroes as suggested here):
import pandas as pd
import numpy as np
from matplotlib.ticker import FuncFormatter
df = pd.DataFrame(np.random.randn(100,5))
ax = df.plot()
ax.yaxis.set_major_formatter(FuncFormatter(lambda y, _: '{:.0%}'.format(y)))
Generally speaking I'd recommend using FuncFormatter
for label formatting: it's reliable, and versatile.