The US president has urged Kenya to hold "visible" trials to tackle corruption, which he said could be the "biggest impediment" tofurther growth.
After talks in Nairobi, President Obama and Kenyan counterpart Uhuru Kenyatta said they were "united against terrorism" and efforts to deal with it.
But the two leaders differed sharply in their positions on gay rights.
While Mr Obama spoke strongly against discrimination, Mr Kenyatta said Kenya did not share the same values.
Earlier Mr Obama praised Africa's economic and business potential in a speech.
"Africa is on the move... People are being lifted out of poverty, incomes are up (and) the middle class is growing," he told a business summit.
President Obama had told the BBC he would deliver a blunt message on gay rights when he travelled to Africa - and defended his stand in response to a question at the joint news conference.
"If somebody is a law-abiding citizen, who is going about their business... and not harming anybody, the idea that they are going to be treated differently or abused because of who they love is wrong. Full stop," he said.
But Uhuru Kenyatta said gay rights were not "foremost" in the minds of Kenyans.
There were "some things that we must admit we don't share - our culture, our societies don't accept," he said.
"It's very difficult for us to be able to impose on people that which they themselves do not accept."
In other comments, President Obama said:
- The US is providing additional funding and assistance to Kenya's security forces for counter-terrorism
- The US and Kenya are working to establish direct flights
- The Obama administration will propose a federal rule banning the sale of almost all ivory across state lines as part of efforts to fight poaching in Africa.