Lewis, 39, was arrested on suspicion of fraud after the District Attorney's Office began investigating the source of funds he used to post $500,000 bail after his Jan. 10 arrest in connection to the fire bombing of an ex-girlfriend's home, said Vacaville Police Lt. John Carli.
"Through this whole process, their investigation has uncovered evidence of fraud ... as it pertains to loans that may be related to the church," Carli said. "So this search warrant is looking into his bail and any other evidence that would tie the church to his bail."
Lewis' uncle, Danny Ray Lewis, 60, who also lives on the property, was also arrested Friday on gun charges after investigators found a weapon with the serial numbers filed off inside the residence, Carli said.
Pastor Lewis was one of four people arrested in connection with the Jan. 9 attack in the 700 block of Chateau Circle. Three Sacramento-area transients arrested near the scene told police they had been staying at his church. Lewis has maintained his innocence to various media outlets.
Though the initial attack is over the Vacaville woman who police say was the intended target of the Molotov cocktail says she and her children are still fearful.
Sarah Nottingham, Lewis' ex-girlfriend, and her three children were asleep inside the two-story home when a firebomb came crashing through an upstairs window around 3:30 a.m.
In a recent email interview, Nottingham said she met Lewis in early 2003 while engaged to her now ex-husband. The couple had been looking for a new church and a pastor to marry them when they stumbled upon Lewis' church.
"We were warmly welcomed at Fellowship Baptist Church and liked Mark's style of preaching," she recalled. "He seemed to have extreme dedication for the Lord."
Following Nottingham's divorce a few years later, she said she left the church so her ex-husband and son could continue attending.
Nottingham said she was in contact with Lewis only a few times through the years, usually about things related to her son's attendance at church.
After hearing about the "tragic" and "unexpected death" of Joanna Lewis in October 2011, Nottingham said she and the pastor reconnected.
They eventually became "best friends," she said and, in October 2012, they became a couple.
"We often talked about the future and even getting married in Michigan, where he was born. Mark was very loving and thoughtful at times but wanted to keep our relationship a secret," Nottingham recalled. "I was told to be patient with that and I was, because I loved him."
Lewis occasionally displayed a quick temper, "but nothing out of the ordinary," she said.
"Things I did notice after about six months I made excuses for," she said, chalking it up to Lewis's grieving after having lost his wife of 13 years.
Lewis seemed to get "more and more controlling," she said, adding that they would go out to eat or shop out of town to avoid running into anyone he knew.
"I grew impatient with waiting for him to let people know about our relationship and he seemed distant. He would lie to church members when asked if we had something between us."
Nottingham said she later learned that Lewis told people that she was suicidal and that he "had to keep me around."
They began to drift apart, and "when I wanted to end our relationship ... he made it clear he wasn't ready to do so," she wrote.
This week she was granted a restraining order against him.
Nottingham said she and her family are holding up, but added, that "it's hard to sleep at night without nightmares or replaying that night over" in her head. She said that she and her children will be starting therapy soon.
"I've lost my job, my car (is) destroyed, and I'm trying to keep my faith in God stronger than before. It really messed with my head that I didn't truly know the person I thought I cared for," she said.
Lewis is slated to make his first court appearance in connection with the firebombing on Jan. 31.