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There were many problems facing Lombard.  To resolve them meant that politics had to be put aside while he re-organised the Irish Church.  Foster writes that, 

“Though the Dublin government would never have believed it, the organization of the Catholic Church in early-seventeenth Ireland was varied, haphazard, informal and uncoordinated.”[43]  

At that time the Irish Church differed greatly from the international Church – it was Celtic and semi-pagan rather than Roman.  There was a great laxity in popular practise.  Local pilgrimages to holy wells and belief in the efficacy of sacred trees and stones proliferated and confession and frequent reception of the sacrament were uncommon.  It was then that Lombard, who was unable to visit his primatial see, appointed the celebrated David Rothe[44] as his Vicar General.  He authorised Rothe to call a provincial synod of the northern dioceses at which a re-organisation of the Irish Church took place.  Significantly the clergy were exhorted to abstain from political matters and to attend to their spiritual ministry.  This was in line with Lombard’s new thinking on relations with the king.  Decrees were also issued dealing with the administration of the sacraments, vestments, when and where Mass was to be celebrated, the spiritual exercises and duties of priests, marriage and the condemnation of superstitions about “holy” trees and wells.

The Archbishop had jurisdiction over all the dioceses that were without a bishop as well as over Armagh.  In this respect we find him granting sacerdotal facilities to priests in various dioceses and, in addition, he granted extraordinary privileges to the clergy on account of the difficulties and dangers that beset them in their ministry.  Priests were not confined to one diocese, they were allowed to minister anywhere they were needed, to say Mass in un-consecrated places, to substitute prayers for the usual Office of the Church.  A major problem in the Irish Church was the absence of bishops and in 1611 Lombard appointed eight new bishops to fill these vacancies.  He appointed bishops to Waterford, Ossory, Limerick, Derry, Ferns, Kilmore, Ardfert and Meath.  However due to the influence of England the consecration of the bishops was delayed for several years.   

After Lombard had appointed Rothe as Bishop of Ossory and Vice-Primate of Ireland, in 1618, the latter convened, in Drogheda, by authority of Lombard, another synod of the clergy of Armagh where the rules and regulations were tightened for the whole Church in Ireland.  In 1622 four sees had bishops appointed, viz., Cork, Limerick, Meath and Emly and in 1625, just a few weeks before Lombard’s death, three other sees in the northern province had their bishops restored.  A Munster synod was held in 1624, at Kilkenny, at which the newly consecrated Bishops of Cork, Limerick and Emly were present as well as the Vicars General of Cashel and Waterford.  The result of this synod was to restore harmony between the regular and secular clergy.

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