The Portuguese has been backed to the tune of some £387 million ($502m) in the transfer market, but old adversaries at the Etihad Stadium have splashed out more than £540m ($701m) over the same period of time.
Mourinho believes sizeable investment has been essential for the Red Devils, with many new players merely acquired to plug the gaps created by the departures of others.
He inherited a squad from Louis van Gaal which had senior figures heading towards the end of their respective careers at Old Trafford, while form and confidence has had to be re-established in others who had lost their way.
Mourinho said ahead of a derby date with City on Sunday: "In my first season I had a situation of players like Wayne Rooney, Michael Carrick - phenomenal players, some of the most important players in past years - going to the end.
"It was hard work with people like Luke and Anthony Martial, for example, because, for these talented players to come to the level that they are, is a process.
"To transform talent in professional players, stability, performance, players is a hard work process. So it is rebuilding, yes."
Mourinho has sought to address supposed weaknesses in his squad by bringing in fresh faces across the field, but he has also faced frustration in the transfer market.
He was unable to land a new centre-half over the summer, despite making that area a top priority, while faith has had to be placed in the likes of Shaw and Martial to come good while rivals have splashed the cash in elaborate splurges.
Mourinho added, with City boss Pep Guardiola having shelled out over £183m ($237m) on Kyle Walker, Benjamin Mendy, Danilo and Aymeric Laporte last season: "If I need a full-back and I buy four, it is easier.
"If I need a full-back because I am not happy with Luke Shaw's level, the easiest thing is to buy four. Some clubs can buy four.
"We didn't buy a left-back for three years, we were wishing and working with Luke to be that left-back.
"But during that process we played Matteo Darmian, we played Ashley Young, we played Marcos Rojo. We didn't buy four.
"There is a difference. To buy four you only need good scouting and money - to make players takes more time."