The Miami Marlins selected Villalobos in the 14th round of the 2018 Major League Baseball draft. Villalobos split his first professional season between three minor league affiliates. In 16 games between the rookie-level Gulf Coast Marlins, Low-A Batavia Muckdogs, and High-A Jupiter Hammerheads, he recorded a cumulative 1-1 record and 6.10 ERA with 19 strikeouts in 20.2 innings pitched. He returned to Batavia in 2019, pitching to an 0-3 record and 6.08 ERA with 48 strikeouts in 47.1 innings of work.
On November 15, 2022, the Marlins added Villalobos to their 40-man roster to protect him from the Rule 5 draft.[2] Villalobos was optioned to the Triple-A Jacksonville Jumbo Shrimp to begin the 2023 season.[3] He struggled to an 11.57 ERA in three appearances before he was designated for assignment by the Marlins on April 9, 2023.[4]
On June 26, 2023, Villalobos was claimed off waivers by the Miami Marlins, marking his second stint with the organization. He was subsequently optioned to the Double–A Pensacola Blue Wahoos.[7] On July 2, Villalobos was again designated for assignment following the promotion of Dane Myers.[8] He cleared waivers and was sent outright to Double–A on July 4.[9]
Villalobos began the 2024 season with Triple–A Jacksonville, recording a 4.73 ERA with 16 strikeouts across 9 games. On May 5, 2024, Villalobos was selected to the 40–man roster and promoted to the major leagues for the first time.[10] In 3 games for Miami, he compiled a 2.08 ERA with 3 strikeouts across 4+1⁄3 innings pitched. On May 27, Villalobos was designated for assignment by the Marlins.[11] He cleared waivers and was sent outright to Jacksonville on May 31,[12] but elected free agency the following day.[13]