In the town of Varese, the high concentration of well-born prelates in the collegiate church of San Vittore had increased the influence of patrician families on the management of San Vittore’s Cathedral.
Therefore, since it was driven and backed up by the town secular authority, the clergy managed almost autonomously the spiritual life of the town and of the surroundings, ignoring and transgressing the dispositions ordered by the Archbishopric of Milan. 
With the appointment of Carlo Borromeo as the new Archbishop of Milan, the situation changed radically. His visit to Varese was definitely not a casual event. On November 11, 1567, during his first pastoral visit to the diocese of Varese, Carlo Borromeo firmly emphasized that the spiritual life of communities was not supposed to be affected by any sort of political or secular pressures at all.
Members of the council of San Vittore in Varese were quite surprised, when they got hastily summoned for a clerical meeting of the Diocese, which the local clergy had disregarded and perhaps forgotten for a long time.
In that consistory, Bernardino Perabò, canon of San Vittore, did not expect his Archbishop to harshly criticize the secular clergy of that Diocese, and did not expect him to blame the same clergy for submitting to the local political authorities and patrician families. Neither did he think that the Archbishop would severely condemn the poor incomes, which in Borromeo’s opinion were caused by the indolence and inefficiency of all the many available prelates. Moreover, the eminent Archbishop judged even more harshly that for more than a quarter of century, no parish priest appointed by the Curia of Milan had had a seat at the Council in Varese.
Bernardino’s defence of the diocesan consolidated condition was doubtlessly inconsequential, neither was he able to oppose Carlo Borromeo’s decision of cutting off the number of councillors of San Vittore from 32 to 18. Following such a severe disciplinary action, the Collegiate was put into the hands of a ‘theological’ priest, who was directly appointed by the Curia of Milan. This office lasted for half-century, and it was still unaltered when Cardinal Federigo Borromeo went to Varese on a pastoral visit. It comes forth no news on Bernardino and the other 14 excluded prelates. Sure thing was the humiliation of the Perabòs family. 
When Carlo Borromeo decided to see Saint John Hospital and Nove Fonti Hospice during his Pastoral visit. Borri writes that Borromeo got a sad and painful impression: the hospital was a decaying and drab building nearby the cathedral, and it did not offer an adequate healthcare service to the indigent. Moreover, neither the municipal authorities, nor the citizens themselves took care of it, and it was run with little incomes of some wills.
Nove Fonti hospice was not in better conditions; it had already been abandoned for a long time, and the administrators did not take care of it any more. It looked crumbling and it lacked any forms of housing and health comforts.
Willing to make a radical change, Archbishop Borromeo summoned the podesta of Varese, the consuls, the town men of Provision, as well as the deans of the hospital. There was no representative of the hospice, since no supervisor had been elected in a very long time. In 1569, Angelo Perabò was appointed as new dean of the hospital, an office that was conceived by the Archbishop himself for a secular member of the Perabòs in order to compensate the shame of San Vittore. The seriousness of the Perabòs commitment showed how important the responsibility of that institute was in town. 
Within such a political and ecclesiastical background, we find the peculiar story of Girolamo Perabò, a distinguished scholar of physics and mathematics, who also loved arts such as poetry and music. Although Pope Pius IV called him to Rome, we have no records of either his life, or of the reasons for his visit in Rome. It is only chronicled that he never made to the Vatican, since he died on the way in 1557. 
In the 16th-century religious scenario in Varese, another extraordinary character makes its entrance, and this time it is a female character: Caterina Perabò, the daughter of Angelo Perabò. When she was still very young on January 11, 1531, she lost her brother Bernardo due to the plague that was spreading out in Lombardy at that time. Afraid of dying of the same epidemic, while she was quarantined at her cousin’s in Paina in the area of Casbeno, on January 19, 1631, Caterina expressed her oral will, which was notified by notary Gian Angelo Maria Castiglioni. She wished to donate to the Hospital Of The Poor half of her belongings in Maccagno, a town not far away from Verbania in the Feud of Counts Mandelli. This donation was bound by the obligation to celebrate “as many masses as needed to spend a quarter of the profits of that gift.”  Destiny was benevolent to her: she had a narrow escape. After her brother’s and father’s dead, she had to administrate the conspicuous family properties that she inherited from them.
Archbishop Borromeo was keen on instituting a convent of nuns in Varese, and decided to fulfil his promise to the Virgins of Saint Ursula during his subsequent pastoral visit. After presenting herself as candidate to the Archbishop, Caterina was elected abbess a se ipsi, in 1584. Immediately, she provided the congregation with an estate in Porta Regondello;  a guest house for all the Virgins of Saint Ursula working at the Hospital of The Poor, and for all those young women, who were keen on being subjected to the jurisdiction of the Diocese without taking the religious vows. In 1587, the convent was provided with a church.  Borromeo’s decision of instituting a secular monastery could appear a little singular in a moment where Caterina Perabò was openly in conflict with the Parish Priest of San Vittore, and the Curia of Milan was trying to consolidate the Church in Lombardy, which was highly centralized and hierarchical. Presumably, aware of the traumatic reorganization of the secular clergy in both the Diocese and in the hospital of Varese, twenty years before, the Archbishop did not want be pitiless against the effort of a local patrician family. In fact, it could be a further shield against the worrying spread of Protestantism in the nearby Ticino area, if achieved according to the prescriptions of the Church.
The second half of the XVI century was characterized by the Spanish political domination in Lombardy. Trying to restore control and a stronger dependence on the central authority of Milan, the new governor of Milan, the Duke of Albuquerque, was interested in abolishing all the benefits that the Viscontis and the Sforzas had granted to Varese. On December 18, 1577, 250 peers and masters of art from the four companies of Varese held a crowed rally to support their political autonomy before the podesta, the Spanish don Giovanni Paciecho, at the Baptistery of Saint John.
The presence of some representatives of the Perabòs such as Giovanni Pietro Perabò, son of Enrico, as Battista, Benedetto and Raffaello Perabò, sons of Andrea, and as Giovanni Alberto Perabò, son of Leonardo.  This massive popular participation mitigated the Spanish unrealistic plans. Therefore, Varese was able maintain its government autonomy unaltered, which it had won from the Viscontis with difficulties. 
Nevertheless, some extra precaution was necessary. Later in 1583, the community of Varese decided to take on a new political and administrative system in order to contain the continuous interferences of the Spanish governor. This new system provided six leaders for the six companies in town, who would work directly with the Spanish podesta. The constitution of such a delegation in the Town council symbolized an important democratic shift, as the leaders had equal powers and were elected by universal suffrage. In 1585, the Council of the leaders was elected for the first time in representation of the town. Clearly, one of the Perabòs – Carlo Alberto – was appointed to become the leader of the Company of Saint Mary. 
However, in addition to some political problems, attention was also focused on the city appearance and its monuments. In the late XVI century, podesta of Varese, the Spanish don Alessandro de Farra, acknowledged the decaying condition of San Vittore’s church, therefore he summoned the town consuls and the leaders of the six companies to the Pretorium.  Following the demolition order, reconstruction started in 1580 directed by the Varese-based architect Giuseppe Bernascone, and it lasted until 1606. During this period, the Perabòs men contributed with a generous handout. Namely, Giuseppe Perabò, leader of the company of Santa Maria, Angelo’s, Cristoforo’s and Giovanni Alberto’s noble families, lastly Nicolao Perabò.