The demonstrations unfolded in Borough Park, one of the neighborhoods forced to restrict capacity at houses of worship and shutter nonessential businesses for at least two weeks starting Thursday, due to surging COVID-19 cases.
Many neighborhoods affected by the new restrictions are home to large populations of Orthodox Jews, and some protesters said the community was being unfairly targeted by the policy.
Much like Tuesday night, images and video shared on social media showed large crowds of Orthodox Jewish men gathered in the streets, with some protesters setting bonfires and burning masks and others carrying Trump flags and signs that said "We will not comply."
Despite the unrest, there were no arrests or summonses issued across both nights, according to the New York Post. However, a journalist alleged that he was attacked during protests Wednesday. Jacob Kornbluh, a reporter for the Jewish Insider, said on Twitter that he was "brutally assaulted, hit in the head, and kicked at by an angry crowd of hundreds of community members of the Boro Park protest -- while yelling at me 'Nazi' and 'Hitler.'"
The NYPD said it was investigating the incident.
On Thursday, Mayor Bill de Blasio called the alleged assault "unacceptable."
"There need to be consequences for that," he said during his daily press briefing.
Officials including NYC Comptroller Scott Stringer and organizations including the American Jewish Committee and the Jewish Democratic Council of America have also called for those responsible to be held accountable.
New York state Senator Simcha Felder, who earlier this week had criticized the governor's move as a "constitutionally questionable shutdown of our communities," condemned the recent violence.
"I am asking, I am begging and I am imploring the handful of people within the community to end the violence," Felder, who represents Borough Park, said in a statement following Wednesday's protests.
In a statement released Thursday by the New York Jewish Agenda in support of the state's and city's measures to limit the spread of COVID-19, more than 400 Jewish religious leaders said they were "embarrassed and disappointed" by the recent unrest. "We are also deeply disturbed by what we have witnessed in the form of mask burnings and large, unsafe, and even violent protests against sensible precautions and regulations," the statement said.
The protests followed Gov. Andrew Cuomo's announcement Tuesday that restrictions would be reinstated in selected hot-spot communities in an effort to slow the spread of COVID-19.
In the top 20 ZIP codes in areas that have seen recent outbreaks -- in Brooklyn and Queens, as well as Rockland and Orange Counties -- the positivity rate of COVID-19 tests was 5.8% on Wednesday, up from 5.1% the day before, the governor's office said. The statewide positivity rate, excluding these ZIP codes, was 1.01% on Wednesday.
The 20 ZIP codes represent just 6.2% of the state's population yet accounted for 23.2% of all positive cases in the state Wednesday, according to the governor's office.
To help people navigate the new restrictions, the city unveiled a color-coded system based on COVID-19 data this week. Restrictions in all zones will be in effect for a minimum of 14 days starting Thursday, the mayor's office said.
In red areas, indicating the most intense clusters, all nonessential businesses are closed. Restaurants are reduced to take-out only, mass gatherings are prohibited and houses of worship are limited to a maximum of 25% capacity or 10 people. Schools had previously closed in red zones this week.
Amid frustrations with the restrictions, Mayor de Blasio said the city is working with community health care providers to help educate people "directly at the grassroots" about their necessity.
He also said there needs to be a "much clearer approach" to how officers respond to the protesters following criticism there has been a lighter police response over the past two nights compared to recent Black Lives Matter demonstrations.
"I expect that to be corrected today before anything that happens this evening," de Blasio said Thursday morning.
In a statement to ABC News, a spokesperson said the NYPD "will continue our education and awareness campaign and will deploy our resources as conditions warrant."
ABC News' Karma Allen contributed to this report.