The 30-year-old won the 100m hurdles in 13.3 seconds before extending her lead with 1.84m in the high jump despite heavy rain falling.
In the third event, Ennis-Hill registered her best shot put mark since winning gold at the London Olympics, launching the put out to 14.29m.
A 200m time of 23.36 earned the overall lead at the end of the first day with the long jump, javelin and 800m still to come.
The event in Ratingen, Germany is only Ennis-Hill’s second outing of the season after she withdrew from June’s multi-event in Gotzis with an Achilles.
It is also the last chance for her to compete in a full heptathlon before heading to Rio to defend her Olympic title.