In a white kurta-pyjama, the visiting premier prayed at the sanctum sanctorum of the temple during an almost hour-long visit to the shrine.
Trudeau was accompanied by his wife, Sophie Gregoire Trudeau, and two of his three children, who were also clad in traditional Punjabi outfits.
The prime minister and his family also tried rolling out rotis at the Guru Ram Das Jee Langar hall, where devotees do voluntary kitchen work for feeding visitors.
They greeted devotees with folded hands while scores of visitors could be seen holding up their mobile phones to take pictures and videos of the Trudeaus.
Punjab police officials and SGPC task force 'sewadars' (volunteers) formed a security ring around the dignitaries. Canadian security officials were also part of their security cover.
Trudeau, along with a delegation of his ministers and MPs, reached the Golden Temple straight from the Amritsar international airport at around 11:55 am.
A red-coloured carpet was laid out for the dignitaries by the Shiromani Gurdwara Parbandhak Committee at the Golden temple complex.
Trudeau and his family took a round or 'parikarma' of the Temple.
The prime minister and his family were given a 'siropa' (robe of honour) inside the shrine.
Among those accompanying the Canadian PM was his defence minister Harjit Sajjan.
Union minister of state (Independent Charge) for Housing and Urban Affairs Hardeep Singh Puri and Punjab Cultural Affairs and Tourism minister Navjot Singh Sidhu also accompanied the Canadian PM at the Golden Temple.
Sikhs constitute a large segment of people of Indian origin settled in Canada.
Later, Trudeau also visited the Partition Museum in the city.
Puri and Sidhu had received the Canadian prime minister and his delegation at the Sri Guru Ramdas International Airport at around 10:40 am.
Amritsar Commissioner of Police SS Srivastva and Deputy Commissioner Kamaldeep Singh Sangha were also present at the airport, officials said.
Shiromani Akali Dal Chief Sukhbir Singh Badal and Shiromani Gurdwara Parbandhak Committee president Gobind Singh Longowal welcomed the visiting PM at the Golden Temple.
Tight security arrangements have been put into effect by the Punjab police in Amritsar with over 1,500 police personnel deployed in the holy city for the visit.
Senior police officials including SSPs and DIGs, besides a SWAT (Special Weapons and Tactics) team, have also been deployed.
The Canadian PM is on a week-long visit to India. Trudeau is accompanied by wife and three children - Ella-Grace, Xavier and Hadrien.
His visit to Punjab had triggered a controversy over reported links between key members of his cabinet and Sikh separatists. Speculation on whether he would meet Punjab chief minister Amarinder Singh was put to rest when it was announced that the two would hold a meeting.
Trudeau will meet Amarinder Singh for a one-on-one meeting at a local hotel. The two are expected to discuss business as well as people-to-people ties.