However, the economic downturn following the Great Hanshin earthquake forced Daiei to pull out and the city of Kobe became responsible for operating the club.

Despite finishing 2nd in the JFL in 1996, Vissel was promoted to the J.League (the champions, Honda FC, refused to abandon their corporate ownership and become a professional club) and began play in the top division of Japanese football in 1997.

In January 2004, Vissel was sold to Crimson Group, parent company of online merchant Rakuten, whose president is Kobe native Hiroshi Mikitani.

Vissel's first signing under the Mikitani regime, İlhan Mansız, who was acquired partly to capitalize on his popularity during the 2002 FIFA World Cup hosted in Korea and Japan, but the Turkish forward played just three matches before leaving the team because of a knee injury.

Alongside Sergi Samper and Andrés Iniesta, Villa was the third Spaniard in the team in that season in which they guided Vissel Kobe to win the 2019 Emperor's Cup.

On 1 January 2020, first time finalist Vissel beat Kashima Antlers in the 2019 Emperor's Cup final at the recently opened New National Stadium to win the first title in the club history.

In 2021, Vissel achieved an historic third place in the table, thus qualifying for the 2022 AFC Champions League yet again in which the club had another good run in the campaign before losing to Korean Jeonbuk Hyundai Motors 3–1 in the quarter-finals.

On 25 November 2023, Vissel Kobe was confirmed as the 2023 J1 League champions for the first time in history, following a 2–1 win over Nagoya Grampus in the second last week of the season.

On 23 of November 2024, Vissel won the second Emperor's Cup of the club history, after a victory over they regional rivals Gamba Osaka in the Kansai Derby.

This synergy between the clubs will also extend to first team level, with the exchange of technical knowledge and coaching methodology together with collaboration in the areas of performance, scouting & recruitment, data analysis and overall squad management."

Vissel Kobe and Górnik Zabrze will work on making the path between Asia and Europe to promote both teams in case of sporting performance and scouting.

The agreement lasted from 1995 to 1996, and during this time, the teams played a home and away exhibition series to fundraise for the relief efforts following the 1995 earthquake in Kobe.

This agreement began with a loan of Kobe player Kaito Yamada to Seattle's reserve squad, the Tacoma Defiance.