Ildefonso was also involved in some controversy after signing with the now-defunct Pangasinan Presidents of the MBA, having a live contract with AGFA and at the same time being selected in the draft. San Miguel had to buy out all his contractual obligations for him to suit up with the Beermen. Ildefonso led the Philippines to a gold-medal in 1997 Southeast Asian Games alongside Rommel Adducul and Ralph Rivera. After a successful amateur career, Danny Ildefonso applied for the PBA draft despite being underage. This prompted the PBA to change their age limit rules, enraging the PBL. Even as Ildefonso entered the draft, he also signed a contract to play for the Pangasinan Presidents of the newly formed Metropolitan Basketball Association. Ildefonso was eventually drafted first-pick overall by Formula Shell in the 1998 PBA draft, but was traded to San Miguel for the Beermen's second overall pick, Noy Castillo, and cash. The San Miguel Corporation franchise wanted the promising youngster in their ranks to be the future cornerstone of the team and this forced them to buy out his MBA contract. In his rookie season, Ildefonso became one of the key players for the Beermen alongside Nelson Asaytono, leading the Beermen to two runner-up finish in the All-Filipino and Commissioner's Cup, losing to Alaska on both occasions. At season's end, he won the Rookie of the Year honors while averaging 11.6 PPG in 74 Games which led all Rookies in 1998. The next season, with the departure of Asaytono and the arrival of Filipino-American rookie Danny Seigle and the performances of imports Terquin Mott and Lamont Strothers, San Miguel won two titles in the 1999 Commissioner's Cup and Governor's Cup, ending a five-year title drought. In 2000, Ildefonso and Seigle would again lead San Miguel to two titles, retaining the Commissioner's and Governor's Cup championships. Ildefonso won the two of the five straight Best Player of the Conference honors and defeated Seigle to win the Most Valuable Player Awards. In 2001, San Miguel defeated sister team Barangay Ginebra Kings, 4-2 to win the All-Filipino Cup. Despite two losses to Red Bull and Sta. Lucia in the Commissioner's Cup and Governor's Cup finals series, Ildefonso went on to sweep the Best Player of the Conference honors and won his second Most Valuable Player Award, joining Bogs Adornado and Alvin Patrimonio as the only players to win the said award on back-to-back seasons.