He already faces a host of challenges: from secular Egyptians worried about his Islamist doctrines; from militants trying to stoke conflict with Israel, and from the poverty and joblessness that fed the Arab Spring and brought down the three-decade dictatorship of Hosni Mubarak.
To all those, add the rising tide of garbage in Cairo, the world's largest Arab city. Morsi declared it one of his top five priorities, promising to clean up the streets within 100 days. In so doing, he gave the electorate a powerful way of measuring his abilities, and it looks increasingly certain that 100 days will be nowhere near enough.
Cairo's waste management problem began to get acute a decade ago as the capital's old system, simple but reliable, became swamped by population growth. A government modernization effort flopped. A swine flu panic prompted the mass slaughter of the pigs that recycled Cairo's organic garbage; the city's metal trash bins were easy prey for thieves, especially during the global scrap metal boom.
In Dar-el-Salam, as in many other parts of the city of 18 million, there is no one to hold back the "nabasheen," the diggers young men and women who rummage through the bags of plastic, glass and cardboard and leave the organic stuff to rot in the streets.
Morsi is wading into a landfill of interwoven problems. Rival collectors vying for the big business of trash fight over turf that used to be parceled out in an orderly way among a fixed number of garbage-collecting clans. Layers of corrupt and inefficient bureaucracy choke the system. The collapse of police forces in the revolution in early 2011 means that no one is enforcing what few rules there are.
As a result, Cairenes end up dumping much of their daily output of 17,000 tons of garbage on the street.
"We have designed an unsustainable system for the city," said Laila Iskandar, an expert in waste management. "It is a chain and no one thinks of the chain. Only the end point ... Out of sight out of mind."
In late July, Morsi launched a "Clean Homeland" campaign, giving free brooms and plastic bags to volunteers from civic groups and the Muslim Brotherhood to which Morsi belongs. They hit several Cairo districts, helped by local authorities, for two days and then turned it into a weekly campaign. They swarm the streets, removing piles of trash. But the garbage quickly returns.
In Ahmed's neighborhood in south Cairo, residents say, the volunteers kept watch for hours to fend off dumpers and diggers. "Even the girls were collecting garbage. The street was sparkling," said Mamdouh Gamea, a dentist. "But it didn't last. It is a matter of behavior."
Waleed el-Senoussi, manager of the Clean Homeland campaign and hygiene file in Morsi's office, said the idea was to define the problems and come up with solutions. The government, he said in an interview, wants to tackle the problem on a national level and issue bids for a more technological system that includes burning waste for energy.
"The big strategy is to turn the garbage from a pain, a burden and a problem into a product that has a market value," he said. "It is unreasonable to solve our problems by going backward."
But experts fear they will trample the traditional systems that have served Cairo well.
The traditional way is that of the zabbaleen, up to 150,000 informal garbagemen who go door to door and collect trash for a minimal fee, transport it to their own neighborhoods and sort out the recyclables. The organic material is fed to pigs. (It's a Christian-dominated industry; Muslims shun the animals.)
The result has been an astounding recycling rate of around 80 percent, and an informal recycling business in which they invested a cumulative $150 million over the past 40 years, according to Iskandar. In Manshiet Nasr, the largest of six garbage cities in Cairo, whole families work at recycling and thousands of workshops produce everything from plastic mats to shoe heels and clothes hangers.
But the zabbaleen couldn't keep up with population growth. So in 2003, the Mubarak government, as part of a failed bid to host the soccer World Cup, contracted international companies to take up garbage collection. But it threw the system into chaos.
The companies worked with dumpsters, but Cairenes didn't use them, having grown used to the zabbaleen coming to their doorstep. Many resented paying both the companies and the zabbaleen. And the zabbaleen resented being squeezed out by the companies. Fights broke out over collecting schedules and routes. Many dumpsters disappeared.
Then came the swine flu panic of 2009. Deprived of their pigs, the zabbaleen no longer had any interest in collecting organic waste.
The end result: The government waste department can't cope, the companies don't have dumpsters or the zabbaleen don't come through. So on any given day or stretch of days a given neighborhood becomes a "no-man's land" of garbage. Instead, there are the diggers, who take what can be recycled and sell it to the zabbaleen, leaving the food scraps strewn on the streets.
The zabbaleen still collect about 8,000 tons more than half the daily output and the companies about 3,000, leaving much of the remaining 6,000 tons on the streets , a lot dumped in the canals and some in the Nile River that flows through the capital.
The surrounding desert makes a useful trash bin and the government operates a half-dozen dumps which anyone can use for a fee. The private companies have their own landfills next to composting plants in outlying cities around Cairo. But only about 3 percent of the trash they gather is recycled, according to a government study cited by Iskandar.
So far, the zabbaleen say, the Muslim Brotherhood and Morsi, like the Mubarak regime, show every sign of ignoring them in favor of developing a new garbage system. They say Morsi's administration didn't consult with the biggest community of zabbaleen about the volunteer clean-up campaign or ask them to be part of it.
"We only heard talk of it," said Romani, a Christian collector in the Manshiet Nasr garbage city, who requested partial anonymity because he fears his community's livelihood is threatened. "It seems they want to take my bread and butter," he said. "This would kill me."
Egypt's Christian minority, around 10 percent of Egypt's 83 million people, as a whole is worried that its livelihood would suffer under Islamist rule but so far the sectarian issue has not overtly come up in the garbage issue. El-Senoussi insists it is not a factor in his government's thinking about modernizing the trade.
Romani was sitting in one of the hundreds recycling workshops that lined the small street of this garbage city. Trucks rumbled in and out. Men and women sat outside their homes amid piles of garbage and mounds of plastic, cardboards and tin cans to be sifted through.
Iskandar, the waste management expert, worries the zabbaleen are sidelined because they are poor and associated with a low-class calling. "These are investors, businessmen," she said. "But (officials) laugh at us. Since they are not companies traded in the stock market and they are not men in suits."
Youssef Farid of Spirit of Youth, an NGO that helps the zabbaleen and is funded in part by the Bill and Melinda Gates Foundation, said sidelining the traditional collectors threatens to repeat previous the government's mistakes.
He said a government representative agreed to meet his group but never showed up. El-Senoussi, who manages Morsi's cleanup campaign, said there was a mixup and no intention of harming the zabbaleen. He said he met with other groups of collectors. "We are dealing with all the stakeholders," he said. "But we must find solutions that develop the system."
Zabbaleen recycling is very basic and only operates in Cairo and Alexandria, Egypt's second city, while the rest of the country has even more rudimentary systems. With the planned reforms, "We are talking about something that would benefit the whole country not just individuals," said el-Senoussi.
"People have a right to a clean life," he said. "We can get rid of garbage and benefit the country."
Back at Ahmed Zaki Street, having dumped their bag of trash, Ahmed's mother, Noura Abdel-Salam, said there was plenty more back home.
"We have to walk all this way ourselves to dump our garbage," she said. "We pay the government and the collectors and end up doing it ourselves."