The 1990s to 2000s saw a major transformation for this church. In 2002, another new church was built. This church could fit 2,200 people, and is one of the largest churches in Malaysia. Work on the new St Anne's Church started in 2000 and was completed two years later. It was opened by the then Apostolic Delegate to Malaysia on 26 July 2002. This church has Minangkabau roofs, truly reflecting the Malaysian culture. Not only was a new church constructed, an avenue named Dataran St. Anne was constructed in front of the church. In view of turning St. Anne's Church into a pilgrim centre, "Domus St Anne" was also built to accommodate pilgrims who intend to stay over. A parish office, parish community centre and presbytery were also built, thus enlarging the sanctuary grounds.