In 1989, Cone took over as the coach of the Alaska Air Force with players such as the famed Bruise Brothers duo of Yoyoy Villamin and Ricky Relosa, and Abet Guidaben. A year later, Cone led the Air Force to the finals of the 1990 PBA Third Conference. Alaska blew a 2-0 lead in the best-of-five series to suffer one of the biggest collapses in PBA history, losing to Purefoods in five games. But in 1991, Alaska won its first championship by defeating Ginebra San Miguel in the 3rd Conference. That team was led by Jojo Lastimosa, Eugene Quilban and Bong Alvarez.
After several struggles, Cone's team would have a strong team of locals Johnny Abarrientos, Jojo Lastimosa, Bong Hawkins, Jeffrey Cariaso and Poch Juinio, while having import Sean Chambers for the Milkmen. From 1994 to 1998, the Milkmen won eight titles in 14 conferences during the stretch. The highlight of that run though would come in the 1996 season when Alaska won the coveted PBA Grand Slam, becoming the third franchise and the fourth team to win a Grand Slam in the history of the PBA.
While Alaska continued to dominate by adding Kenneth Duremdes in 1997. Duremdes, playing a limited role with the Pop Cola franchise, rose up to the occasion in 1998 under Cone's tutelage, winning the PBA Most Valuable Player Award at 24 years of age. That year, Cone was hired as the coach of the Philippine Centennial Team led by Duremdes, Abarrientos, Lastimosa, three players on Cone's Alaska team, and PBA stars Alvin Patrimonio, Marlou Aquino and Allan Caidic. That team won a bronze medal in the 1998 Asian Games in Bangkok, Thailand.
Alaska won the 2000 All-Filipino Cup, but afterwards, the team faced rebuilding and traded away several remnants of the old Alaska. Cone, however, would lead the young team of John Arigo and Ali Peek to runner-up finishes in the 2002 Governors and All-Filipino Cup. A year later, the Aces added UAAP star Mike Cortez and Brandon Cablay, leading Alaska to the 2003 PBA Invitational Cup championship, Cone's 11th title.
On July 17, 2006, Manila Standard reported that after his 22 years of service Alaska is set to terminate Cone depending on a meeting between both parties after Cone's contract with the Aces expired on July 15. Rumors also speculated that his replacement will be his former assistant, former National team mentor Chot Reyes, with Cone staying on as team consultant. 
However, a day later, the Aces' official website reported that Cone has agreed to a new deal to stay on as the team's head coach for the 2006-07 PBA season. Terms of the contract were not disclosed.
B-Meg Llamados/San Mig Super Coffee Mixers (2011-present)
On September 1, 2011, Alaska team owner Wilfred Uytengsu announced that it has "released Tim Cone as head coach of the Alaska Aces" after his 22 years of Service for the Alaska Aces Uytengsu remarked that Cone requested to be released a week earlier. Cone was quick to deny in a press conference that he is set to coach B-Meg Llamados, another PBA team.
On September 14, 2011, Tim Cone was at the B-Meg Llamados practice that day and was introduced as the new head coach. He tapped former Alaska players Johnny Abarrientos and Jeffrey Cariaso as assistant coaches. The two new assistant coaches were joined by current assistant coach Koy Banal.
On October 25, 2013, the Llamados, now named as San Mig Super Coffee Mixers, under Cone's tutelage, won the PBA Governors Cup championship, after beating Petron Blaze Boosters. By winning the season-ending best-of-seven series 4-3, the former Purefoods ballclub won its second championship over the last five conferences and more importantly the career 15th title for Cone, putting the veteran coach in the company of the great Baby Dalupan at the top of the all-time list.
On February 26, 2014, Cone won his 16th PBA title as he guided the Mixers to their 11th title against the Rain or Shine Elasto Painters. They beat the E-Painters in six games. With this win, he broke legendary Baby Dalupan's record. On May 15, 2014, San Mig Coffee Mixers beat the Talk N' Text Tropang Texters in Game 4 of Best of 5 series, where San Mig earned the rare 3 peat. This championship gives Tim Cone his 17th PBA Title. He clinched his 18th title, also made history by being the first mentor to win two Grand Slams after he steered San Mig Coffee to pull off a historic Grand Slam and a fourth straight championship in the 2014 Governors’ Cup.
Cone was born in the United States and grew up in Oregon. He moved to the Philippines when he was nine years old after his father came to the country to work in the logging industry. He, along with his mother and sister, moved to Manila. He and his sister were enrolled in the International School Manila, where he eventually finished high school. He went on to attend college in the US, spending two years at Menlo College in California where he played basketball, before moving to George Washington University where he eventually graduated. He says he had never thought of a career in basketball because “when you’re growing up as a young man, you don’t dream of being a coach.”