After retiring, he began his managerial career with Deportes Tolima, before being named in charge of Santa Fe in August 1993.
[1] After managing Deportes Quindío and Venezuelan side Minervén, Boyacá returned to Santa Fe in 1999 to take over the youth categories.
On 18 August 2010, after a period back at Santa Fe as an assistant, Boyacá was named manager of Unión Magdalena.
[6] He opted to leave the club in December to join Germán González [es]'s staff at Venezuelan side Deportivo Lara,[7] but returned to his home country in the following year to take over Santa Fe.
[12] On 7 January 2019, Boyacá returned to Santa Fe as manager of the youth categories,[13] but left the club in July.