[1] He studied at Franciscan College of St. Anthony in Leuven, where he joined the Friars Minor, and acquired Jansenist sympathies.
Those opposed to the Treaty included militant Catholic clergy led by the Papal Nuncio Rinuccini) who wanted Roman Catholicism established as the state religion in Ireland and Irish lords, such as Owen Roe O'Neill, who wanted to recover the lands and power their families had lost after the Plantations of Ireland.
All Catholic clergy captured by the Cromwellians were executed and Walsh, in danger of death, fled Ireland, first to London, then Madrid, and Holland.
Walsh endeavoured to mitigate their lot and efface the impression made by their successive rebellions by a loyal remonstrance to Charles II, boldly repudiating papal infallibility and interference in public affairs, and affirming undivided allegiance to the crown.
For eight years he canvassed for signatures to this address, but in spite of considerable support, the strenuous opposition of the Jesuits and Dominicans deterred the clergy and nearly wrecked the scheme.