In a wide-ranging state of the union speech to MEPs in Strasbourg on Wednesday, he acknowledged that the state of Europe today, as was the case a year ago, "left a lot to be desired" and could be seen as a "colourless melting pot."
But the former Luxembourg Prime Minister, who outlined a number of new legislative initiatives, including a European solidarity fund, insisted that the EU could still be a "champion" for EU citizens.
He said, "I accept, however, that we need to better explain the EU. Citizens will not fooled. They want to see clear results."
The EU, he said, had brought "huge if often invisible" benefits, not least economically and boosting employment.
"However, it is not just about defending the EU but empowering those, including the young, who live in Europe."
Juncker said he had asked the Commissioners to visit national parliaments to spell out the merits of the EU, including eight million new jobs created in the past year. He added, "They have done this 350 times, but we need to do it more often."
He also said, "Some say we lock ourselves in an Ivory Tower in the Berlaymont (the Commission headquarters) and do not listen to people, but that is a mistaken view. We do listen to citizens but we need to listen more intensely."
He countered suggestions that the EU wanted to undermine member states, saying, "This is not about getting rid of nation states and we do not want to destroy member states."
However, Juncker - who received sporadic applause during his long-awaited speech - argued that the current crisis facing the EU was a primary reason for the "galloping populism" present across Europe.
"Populism, though, does not solve our problems. It creates problems," he told a packed chamber.
Juncker refuted attacks from groups such as Ukip that he was a "blind fanatic" and that his speech could be compared with the US President's annual of the union address, because Europe was "more diverse" than America.
In his address, coming ahead of Friday's informal summit in Bratislava, Juncker said "many had forgotten what being a good European means."
He added, "I am convinced that the EU is worth preserving, but have the impression many have forgotten why we chose to work together in the first place, the 70 years of peace and our pride in the EU flag."
"Of course, we still have our differences but, today, we fight these with words, not in the trenches."
He was scathing of recent attacks on Polish nationals in the UK since the EU referendum.
In one incident, Arkadiusz Jozwik was badly beaten and killed on 27 August.
Following the 23 June referendum, when Britain voted in favour of leaving the EU, there appears to be a rise in crimes of this nature. These incidents included the vandalising of a Polish community centre in west London and the distribution of cards reading "no more Polish vermin" in Cambridgeshire.
On this, Juncker said, "It is totally unacceptable that Polish people are being harassed, attacked and even killed on the streets of Essex. The EU is not the Wild West."