So the data you want is here:
WolframAlpha["p/e msft 1/3/2000 to 6/1/2000"]

How can it be accessed? Assuming you want the data from the plot, you need to see what the name of the pod you are interested is,
WolframAlpha["p/e msft 1/3/2000 to 6/1/2000", "PodIDs"]
(* {"Input", "Result", "DateRangeSpecified:PriceEarningsRatio:FinancialData"} *)
That last one is what we are looking for, so we look a little deeper
WolframAlpha["p/e msft 1/3/2000 to 6/1/2000", {"DateRangeSpecified:PriceEarningsRatio:FinancialData"}]

That one labeled "TimeSeriesData" looks intersting,
`WolframAlpha["p/e msft 1/3/2000 to 6/1/2000",
{"DateRangeSpecified:PriceEarningsRatio:FinancialData",
"TimeSeriesData"}]

Bingo! That's what you need,
data = {{"DateRangeSpecified:PriceEarningsRatio:FinancialData", 1},
"TimeSeriesData"} /.
WolframAlpha[
"p/e msft 1/3/2000 to 6/1/2000", \
{"DateRangeSpecified:PriceEarningsRatio:FinancialData",
"TimeSeriesData"}];
DateListPlot[data]

This method is not foolproof - it seems that you can't enter a time period over a certain length and still get a "TimeSeries" result, so toy around with it. For example, the string "p/e msft 1/3/1990 to 6/1/1991" gives a result but "p/e msft 1/3/1990 to 6/1/1992" does not. Also, try adding TimeConstrained -> 120 as an option to WolframAlpha to avoid timeouts.
data=WolframAlpha["p/e msft 2000/1/3 to 2000/3/15", \ {{"DateRangeSpecified:PriceEarningsRatio:FinancialData", 1}, "ComputableData"}]; DateListPlot[data]? – kglr Jul 07 '16 at 21:29data = WolframAlpha["p/e msft 2000/1/3 to 2000/3/15", \ {{"DateRangeSpecified:PriceEarningsRatio:FinancialData", 1}, "TimeSeriesData"}]– kglr Jul 07 '16 at 21:32