Cork: 1986–1996 Morgan first got a taste of inter-county managerial experience in his last championship season when he was player-manager with
Cork. His period in charge ended with defeat in the Munster final of 1981. Five year later in the autumn of 1986 Morgan was appointed Cork manager for a second time. The task ahead was enormous as Cork's nearest neighbours, Kerry, had won eleven of the last twelve Munster titles and had put Cork to the sword on most of those occasions. In his first year in charge Morgan worked the oracle. The traditional Munster final between Cork and Kerry ended in a draw, however, Cork triumphed over the four-in-a-row hopefuls by 0–13 to 1–5. Cork subsequently qualified for the All-Ireland final with Meath providing the opposition. Midway through the first-half Cork had a goal chance blocked by
Mick Lyons when
Jimmy Kerrigan looked to be through for a seven-point lead. Instead, it was Meath who led by 1–6 to 0–8 at half-time, courtesy of a
Colm O'Rourke goal. Cork's
Larry Tompkins's radar was also off course as he missed six out of eight free-kicks. At the full-time whistle Meath were the winners by 1–14 to 0–11. In 1988 Morgan's team retained their Munster title before a second All-Ireland final appearance beckoned. Meath provided the opposition once again as Cork got off to a good start with a
Teddy McCarthy goal. By the end of the game Cork led by a point, however,
Brian Stafford scored the equaliser. The replay was a controversial affair. Meath's
Gerry McEntee was sent-off after just seven minutes. In spite of being reduced to fourteen men, Meath hung on for a narrow 0–13 to 0–12 victory. It was Morgan's first All-Ireland title as manager and Cork's first since 1973, when Morgan was captain. In 1990, while still under Morgan's guidance, Cork made it a remarkable four Munster titles on the trot. A fourth consecutive All-Ireland final appearance quickly followed, with old rivals Meath providing the opposition. Cork suffered a blow in the first-half when
Colm O'Neill was sent off; however,
Shay Fahy was playing a blinder at midfield. In spite of only having fourteen men Cork won the game by 0–11 to 0–9. It was a second consecutive All-Ireland title for Morgan, the first time that Cork had achieved the feat. This victory was all the more special as the Cork hurling team had already won their respective
All-Ireland title a fortnight earlier. It was the first time in the modern era that a county had won the hurling and football '
double'. In 1991 Cork lost their provincial crown to Kerry and Morgan faced a year of difficulties with the Cork County Board. For a period it looked as if he might resign, however, he stayed on only to face defeat again in 1992. Once again the knives were out for him, however, Cork won back to Munster title in 1993. Cork subsequently qualified for the All-Ireland final, with
Derry providing the opposition. Things did not go to plan as 'the Rebels' were reduced to fourteen men when
Tony Davis was harshly red-carded.
Séamus Downey scored the winning goal as Derry secured their first All-Ireland with a 1–14 to 2–8 victory. In 1994 Morgan managed Cork to a second consecutive Munster winners' medal following another convincing victory over
Tipperary. Cork, however, were later defeated by eventual champions
Down in the All-Ireland semi-final. In 1995 Morgan's Cork won a third consecutive Munster title, a record-breaking seventh in nine seasons, as Kerry fell in the provincial decider. Once again Cork were subsequently defeated by eventual All-Ireland champions
Dublin in the All-Ireland semi-final. In 1996 the old order in Munster was restored. Kerry defeated Cork by 0–14 to 0–11 in the Munster final, taking their first provincial title since 1991 in the process. This defeat saw Cork exit the championship and effectively brought Morgan's ten-season tenure as manager to an end.
Nemo Rangers: 2000–2003 Morgan has been involved in coaching various Nemo Rangers teams at all levels; however, in the late 1990s he took charge of the club’s senior football team. In 2000 Nemo Rangers broke back after a six-year absence and won the county senior championship following a ten-point defeat of divisional side
Carbery. Nemo later represented Cork in the provincial club championship and even reached the final of that competition. A 0–11 to 0–7 defeat of
Glenflesk gave the club another Munster club winners' medal. Morgan subsequently guided his team to a foot-and-mouth delayed All-Ireland club final, with Mayo's
Crossmolina providing the opposition. Nemo looked to be in the driving seat, however, a second-half comeback, inspired by
Kieran McDonald, saw the momentum switch to the Mayo side. A late
Colin Corkery goal narrowed the deficit to one point, however, Morgan's side were eventually and narrowly defeated by 0–16 to 1–12. In 2001 Morgan coached Nemo to a second county championship title as the club trounced
Bantry Blues in the final. A second Munster club winners' medal was quickly captured, after a 1–11 to 0–10 defeat of
Fethard. Morgan's side subsequently lined out in his second All-Ireland club final, this time with
Ballinderry providing the opposition. The championship decider was switched to
Semple Stadium because of the reconstruction of
Croke Park, however, a change of venue did not suit Nemo. Goals by
Gerard Cassidy and
Declan Bateson gave the Derry side a comfortable 2–10 to 0–9 victory. It was a second consecutive All-Ireland defeat for Nemo. Morgan had finally secured a Munster winners' medal with his new team. The quirks of the championship saw Cork face Kerry again in the subsequent All-Ireland semi-final for the second year in-a-row. In a similar pattern to the two previous encounters Cork failed to beat Kerry at Croke Park. A 0–16 to 0–10 resulted in Morgan's side being dumped out of the championship. In 2007 Morgan's Cork narrowly lost their Munster crown to Kerry. In spite of the 1–15 to 1–13 defeat Cork still had another chance to claim the All-Ireland title. Cork later did well in the All-Ireland series and finally qualified for the championship decider. It was the seventh time that Morgan was aiding a Cork team in an All-Ireland final, either as a player or as a manager. Kerry, however, were the opponents. While the first half was played on an even keel, 'the Kingdom' ran riot in the second half and a rout ensued. At the full-time whistle Cork were trounced by 3–13 to 1–9. Morgan subsequently stepped down as Cork football manager. ==Honours==