While more than one million students attended online, about 90,000 younger and special education students headed back to their classrooms for in-person learning.
There are some staffing problems, in part because the number of families opting for in-person learning is dropping week by week.
With 3K, pre-K and special ed students returning to classrooms Monday, the rest -- who opted into to in-person learning -- are expected to return next week.
The city continues to work on staffing plans after announcing a second delay last week, with the intention of bringing in an additional 4,500 teachers.
Mayor Bill de Blasio said more teachers might be needed, but he couldn't give an exact number.
He said that's because parents continue opting their kids in and out of in-person learning, and some teachers are also opting out of in-person instruction.
The city is still working to get everyone back in the classroom next week.
There is a "real heavy emphasis on the cleaning, the ventilation, the PPE, any last minute problems being addressed really quickly, and then making sure the staffing is moved where it needs to be," de Blasio said.
Meantime, at one school - IS 131 in Soundview, Bronx - they returned to classrooms Monday, but everyone stayed at home Tuesday.
The change comes after administrators learned that two staff members tested positive for COVID-19 over the past seven days.
In-person learning is expected to resume there on Wednesday.
RELATED: Stay informed with ABC7's NYC COVID-19 positivity rate tracker
MORE INFO: NYC Department of Education
Here are the city's current back-to-school details:
On Monday, 3-K, Pre-K, and early education sites will open including District 75 for special education.
Children who are enrolled in fully remote programs will still begin full-day instruction.
Children in blended learning will be learning remotely until their in-person start date.
All Elementary Schools (K-5 and K-8) including students in Grades 6-8 in K-8 schools: In-Person Learning begins on Tuesday, September 29
Middle Schools (Grades 6-8): In-Person Learning begins on Thursday, October 1
High Schools (Grades 9-12): In-Person Learning begins on Thursday, October 1
Secondary Schools (Grades 6-12): In-Person Learning begins on Thursday, October 1
Transfer Schools, Adult Education, Evening Schools: In-Person Learning begins on Thursday, October 1
K-2 and K-3 Schools: In-Person Learning begins on Tuesday, September 29
Stay informed with ABC7's NYC COVID-19 positivity rate tracker
Grades K-8: In-Person Learning begins on Tuesday, September 29
Grades 9-12: In-Person Learning begins on Thursday, October 1
RELATED: New York, New Jersey, Connecticut out-of-state travelers quarantine list
MORE CORONAVIRUS COVID-19 COVERAGE
Back to school information
How coronavirus changed the New York region
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What's Open, What's Closed in the Tri-State area
COVID-19 Help, Information. Stimulus and Business Updates
New York City
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abc7NY Phase Tracker: