Just before the meeting, Ardern said at her weekly press conference Indonesia was an important potential economic partner for New Zealand as the largest nation in the Asean grouping.
She said bilateral trade was at about $1.8 billion and the goal was to lift that to $4 billion by 2024.
"It is our view that more can be done to try and lift our sights in terms of our trade relationship."
She said she would raise human rights issues as previous governments had done. That included issues of freedom of speech and the access of foreign media in the Papua region.
She would also raise the issue of the overhaul of a Criminal Code in Indonesia which could result in homosexuality and sex before marriage being banned.
The National Party leader Simon Bridges also met with Widodo, accompanied by National MP Kanwaljit Singh Bakshi who is chair of the New Zealand Indonesia Parliamentary Friendship Group.
Widodo congratulated Bridges for his recent appointment as National Party leader.
Through an interpreter, Widodo said he hoped relations would grow further "based on mutual trust and benefit".
"And also allow me to applaud New Zealand's support of Indonesia's territorial integrity," Widodo said.
The media were ushered out of the room as Bridges started his response.
While many visiting international leaders and ministers hold press conferences, there was no press conference on Widodo's visit.
Ardern said that was partly because of logistics but was also decided after consultations on both sides on a case bu case basis.
Foreign Minister Winston Peters and Defence Minister Ron Mark also attended the meeting in the Beehive.