Us Weekly confirmed the 23-year-old model and 25-year-old singer recently broke up after reconciling in the spring.
"They're done," a source said. "They could get back together, but it's over for now."
Another insider said Hadid and Malik "tried hard to make it work" but weren't able to get past certain issues in their relationship.
"She cut herself off from all her friends every time they were together," the source said. "She focused all her time and energy on him, but it just got to be too much."
Entertainment Tonight also said Hadid and Malik struggled to make their relationship work the second time around.
"Gigi and Zayn have broken up, but not because they don't love each other," a source said. "Zayn has been dealing with personal things for a while and Gigi has become a comfort blanket for him."
"Gigi will always support him but she has realized only Zayn can help Zayn," the insider added.
Hadid and Malik have yet to publicly address their split, although Malik posted a moody selfie Wednesday in a sunny location. The former One Direction singer did not include a caption.
Hadid and Malik initially split in March after two years of dating. Malik said in the July issue of GQ that he doesn't label his relationship with Hadid.
"We're adults. We don't need to put a label on it, make it something for people's expectations," he said.