I was also curious about this. The documentation is not very clear about the fact that you need to also change the alias of history to display timestamps, as pointed out by @eremit above (comment #4).

TL;DR I got this working (with seconds) in the end like this:

comment out the line about HIST_STAMPS
add the following alias: alias history='fc -t "%Y-%m-%d %T:" -il '

For completeness, this is how I changed my .zshrc:

# Uncomment the following line if you want to change the command execution
# timestamp shown in the history command output.
# The optional three formats: "mm/dd/yyyy"|"dd.mm.yyyy"|"yyyy-mm-dd"
# HIST_STAMPS="yyyy-mm-dd hh:MM:SS "
# with this setting you need this alias (by default history is aliased
# to 'fc -l 1').  
# alias history="fc -il 1"

# However, if you also want seconds, the solution above doesn't work as
# you would expect.
HIST_FORMAT="'%Y-%m-%d %T:'$(echo -e '\t')"
alias history="fc -t "$HIST_FORMAT" -il 1"

note that I defined a variable HIST_FORMAT for ease and because I also wanted to add a \t to be printed between the timestamp and the command.

How do you display seconds in time? #6109

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