A Brooklyn man was charged with setting fire to a building housing a synagogue and a yeshiva, and federal prosecutors said on Saturday that it was the second time in less than a week that the man had sought to damage a religious institution.

The man, Ali Alaheri, 29, was accused of carefully arranging and then igniting piles of garbage bags on Wednesday near the side of the building that housed the synagogue and the yeshiva.

Hours later, on the same block in the Borough Park neighborhood, Mr. Alaheri approached a Jewish man, who was described in court documents as wearing “traditional Hasidic clothing,” and punched him multiple times in the head. A description of the man’s injuries was not provided.

Mr. Alaheri was also accused of defacing a Catholic church and of attacking a Black man in a New York City subway station this month. He was arrested on Friday in Dobbs Ferry in Westchester County, the police said, and appeared to be in possession of a stolen bicycle.

Ashley Burrell, a lawyer for Mr. Alaheri, who appeared virtually in court on Saturday afternoon, declined to comment.

If convicted of the arson charge, Mr. Alaheri could face up to 20 years in prison. Federal prosecutors said they were not pursuing hate crime charges against Mr. Alaheri; they declined to say why.

The accusations against Mr. Alaheri came a day after another man in Brooklyn was arrested on hate crime charges after a Jewish man was hit and beaten by several others while he lay in the street.

Jewish organizations have raised concerns over research that shows that both face-to-face and online cases of anti-Semitism have risen across the nation alongside the conflict in the Middle East.

In New York, at least 27 people were arrested after clashes erupted in Midtown Manhattan on Thursday between pro-Israeli and pro-Palestinian demonstrators.

One man faces charges, including assault as a hate crime, after he was accused of attacking a 29-year-old Jewish man, Joseph Borgen, who was punched, kicked, pepper-sprayed and hit with crutches by a group of several people as he lay in the street.

Mr. Borgen left the hospital early on Friday morning. The police said they were looking for five to six other people in connection with the assault.

In the charges against Mr. Alaheri, prosecutors said he had “meticulously lined up piles of garbage bags” outside the door of the building on 36th Street in Brooklyn early in the morning.

He is accused of then setting the bags on fire, and court documents say that “it is clear from the manner in which the defendant placed the bags in a line against the yeshiva’s door that he intended the fire to damage or destroy the yeshiva.” The extent of the damage was not described in court records.

Hours later, Mr. Alaheri attacked a Jewish man who was near the building and sitting outside. He took the man’s cellphone before later dropping it, court records said.

Five days before the synagogue and yeshiva fire, Mr. Alaheri defaced a Catholic church, federal prosecutors said.

At St. Athanasius Roman Catholic Church in the Bensonhurst neighborhood of Brooklyn, he set fire to an American flag outside the building on May 14, court documents said.

Mr. Alaheri can be seen on surveillance video later walking in the direction of a cross and a statue of Jesus. The next morning, they were found toppled, court documents said.

Another statue of Jesus at the same church was also found defaced with markings from a hammer. A man matching Mr. Alaheri’s description was seen hours earlier carrying a hammer as he attempted to steal a bicycle in the area, court documents say.

Mr. Alaheri is not facing federal charges related to what happened at the church. The Brooklyn district attorney’s office said it was not pursuing charges against Mr. Alaheri.

Msgr. David Cassato at St. Athanasius said on Saturday that a parishioner had called him early in the morning to an outdoor shrine, where he first noticed the damage.

“A million thoughts and feelings went on inside of myself, from anger, to rage, to hurt to the whole question of who would do such a thing,” Monsignor Cassato said, adding that the Bible verse “Father, forgive them for they know not what they do” had come to mind.

“It really ripped me tremendously,” he added.

In unrelated episode, officials said that Mr. Alaheri had punched a Black man as he stood in an unspecified New York City subway station on May 5. The two had not had any prior interactions, court documents said.

Federal prosecutors said that video evidence connected Mr. Alaheri to each of the episodes.

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