Shortly after his return to England his direct supervision of St. Joseph's College was brought to an end by his appointment as Bishop of Salford on 22 October, 1872. This necessitated his relinquishing direct management of the college at Mill Hill. He then appointed his secretary, Canon Peter Ludovico Benoit as rector (1872-1892). Benoit had become the first Flemish missionary to England in 1847 and was well known to Vaughan through his relatives in Lancashire. Benoit gave up his title on his acceptance, but continued to be addressed in honorary form as canon throughout his life. Benoit was to remain at St. Joseph’s College for almost twenty years, earning from Vaughan the titles of ‘the true founder of this house’, and ‘the second founder’ of St. Joseph’s Missionary Society. But though St. Joseph's now had its local superior, Vaughan, to the end of his life, was the head of the Missionary Society. He may have done more conspicuous and important work in his life, but there was none that was dearer to his heart than the founding of this great college, which is still doing the things he planned.
In those early days, aspiring missionaries who had not completed their secondary education were boarded out at existing apostolic schools, until Vaughan and Benoit recognized the need to establish their own preparatory seminary. Beginning at Coedangred on Monmouthshire in 1880, the satellite community moved to Kelvedon in Essex in 1883 and finally settled at Freshfield, near Liverpool, in 1884. Bishop Vaughan dedicated the minor seminary to St. Peter, the ‘fisher of men’, and called the young students ‘Peter Boys’.
From the beginning, Vaughan was aware that his young society could not rely on the relatively sparse Catholic population of England to supply candidates in sufficient numbers for the missionary apostolate he had in mind. Before leaving Mill Hill for Salford, he made a tour of seminaries in Holland to make the existence of his society known and hopefully ‘land some fish’. Canon Benoit made similar efforts to recruit Dutch candidates, and Vaughan, as Bishop of Salford, visited Holland a second time in 1876 and had lengthy conversations with local bishops. As a result, numbers of candidates began to offer themselves for the missionary apostolate, and a seminary was established in 1890 at Roosendaal in North Brabant.
Even before the new seminary had opened in Holland, Vaughan had set his sights on the Austrian Tyrol which he had visited in 1855 as a guest of the Schonberg family at Castle Pallus near Brixen. In 1890, on his way to Rome, he interrupted his journey to meet the Bishop of Brixen as well as the Governor of Tyrol, both of whom encouraged his enterprise. In May 1891 a seminary was opened in rented accommodation near the Brixen railway station, the forerunner of the purpose built Missionshaus that began in the year of the Founder’s death.
Among the results of Vaughan's first visit to the United States must be reckoned a new appreciation of the power of the Press. He came back resolved to own a paper of his own, and eventually bought "The Tablet". It proved a fortunate investment from every point of view. During the time of the great controversy which preceded the definition of papal infallibility, under the direct editorship of Herbert Vaughan "The Tablet", for services to the Catholic cause, received the special thanks of the Holy See.
The Pastoral Seminary
As bishop, Vaughan worked tirelessly to further the Catholic cause in England. Vaughan’s first concern was for ecclesiastical education and the proper supply of priests for the diocese. The seminarians were scattered about in different colleges, some in England and some abroad. When they had completed their theological studies at Ushaw, or in Rome, Paris, Valladolid, or Lisbon, they returned to the diocese almost as strangers to each other and to their bishop. Bishop Vaughan proposed to establish a transitional pastoral seminary. It was to be attached to his own house, and when clerical students came from Ushaw or seminaries abroad, they were to live with him for a year and, while continuing their ecclesiastical studies, were to be trained by experienced priests in the practical work of a parish. The bishop explained that he had no money for building but his personal enthusiasm for this project was sufficient to win both moral and financial support from laity and clergy alike and it was not long before Cardinal Manning was laying the foundation stone of the Pastoral Seminary.
The support Vaughan’s experimental seminary attracted was a testimony to its good sense. The parishes, however, began to call more and more on the services of young priests who had not completed their pastoral training, making it increasingly difficult to guarantee the seminary’s future. One of the final actions of Vaughan as Bishop was to bring the experiment to a formal end.