About 1589 he went into partnership with the royal favourite Sir Walter Ralegh (qv), as well as with two merchants, Edward Dodge and Veronio Martens, for the export of timber from the woods on Ralegh's vast estates in Munster. Pyne oversaw this operation and Ralegh granted him a forty-one-year lease of land at Mogeely, Co. Cork, which became his new residence. This was by far the most ambitious commercial enterprise yet attempted in Ireland, requiring an investment of over £5,000. The trees were cut down in the woods at Mogeely and Kilcoran and brought to the sawmill at Mogeely castle, where they were manufactured into wooden caskets; these caskets were conveyed by horse or by hand for three miles (5 km) to the Blackwater river and floated downstream to Youghal for shipment abroad. Raleigh had procured special licence to export to any destination, and by far the best markets for these caskets were the relatively treeless Spanish islands of Madeira and the Canaries; a somewhat politically sensitive commerce, given that England and Spain were then at war. During 1590–92 about 340,000 caskets were sold abroad and about 200 men, mostly English settlers, were employed in the enterprise, which stimulated the economies of east Cork and west Waterford.
This venture had only been made possible by the confiscation of property associated with the plantation of Munster, but Pyne shrewdly sought to neutralise any bitterness among the local Irish by cultivating the neighbouring native landowners. One of these, Patrick Condon, was engaged in a bitter and prolonged legal action with an English planter, Arthur Hyde, for possession of large tracts of land. In return for Condon's assistance regarding his timber business and a favourable 101-year lease of some of the disputed land, Pyne and Ralegh used their influence to help Condon's eventually successful bid to retain his property. Pyne's championing of Condon alienated many English settlers in the province as well as leading members of the royal administration. He also became close to David Barry (qv) and even James fitz Thomas Fitzgerald (qv), who regarded himself as the rightful heir to the former territories of the earls of Desmond which had been confiscated as part of the Munster plantation, and included the land occupied by Pyne at Mogeely.
The lord deputy, Sir William Fitzwilliam (qv), resented the privileges granted to Ralegh's colony and generally feared the influence of royal courtiers. Thus, he pounced on the opportunity provided by Ralegh's fall from royal favour (1592) to harass and extort money from Ralegh's tenants. Then in late 1592 he banned the export of timber from Ireland, effectively shutting down Pyne's operation, and, in February 1593 had Pyne arrested and imprisoned in Dublin Castle on suspicion of having exported barrel staves and planks suitable for shipbuilding to mainland Spain, and of having relayed information between catholics in Ireland and in Europe. He also insinuated that Pyne was engaged in sinister machinations with Condon, who was a former rebel. Sent to London in July 1593, Pyne was examined by the privy council, which exonerated him. By August he was petitioning in London to be allowed to resume his trade, to which the crown assented (January 1594), while stipulating that he could only export to the Canary Islands, Madeira, La Rochelle, and Bordeaux. These appear to have been his prime markets, so he and his partners lost little by this restriction. This dispensation effectively gave them a monopoly on the export of timber from Ireland, given that Fitzwilliam's previous blanket ban on this trade remained in force. In June 1596 Pyne acquired the authority in Munster to enforce crown regulations governing the export of timber and the exploitation of Ireland's woods, which empowered him to suppress his competitors in the province. The most significant of these would appear to have been the merchants of Waterford city, who were the main victims of an English privy council injunction of December 1596, prohibiting the export of any wooden caskets from the ports of Waterford and Duncannon.
Although the enterprise seemed set fair eventually to recoup its owners’ mammoth capital investment, Pyne's relationship with his business partners, particularly Ralegh, was far from harmonious. On Pyne's coming to Munster, Ralegh had indicated that he would receive a lease of the entire manor of Mogeely, but instead leased most of this manor to two other tenants, leaving Pyne with the castle and a mere 1,000 acres. In order to placate Pyne, Ralegh granted him an eighty-year extension to his existing lease. Moreover, Ralegh was not always an effective court patron, as evidenced by Pyne's spell in prison during 1593 and by Ralegh's failure to fulfil his promise to procure an absolute guarantee of Patrick Condon's rights to his estates, something that embarrassed Pyne. In 1595 Ralegh sent two agents to Munster to establish iron-ore factories on his estates, but encountered resistance from his pre-existing tenants. Presumably Pyne did not want the operators of this factory, who would need much timber for fuel, driving up the price of timber exploitation rights, and he took part in this opposition. Meanwhile, he also invested in developing his land at Mogeely and the property he leased from Condon, on which he settled a small but flourishing English colony.
Immediately prior to the outbreak of an uprising in autumn 1598 that consumed most of Munster, Pyne left Ireland, bringing his family and possessions in tow. Many of his fellow English suspected that his friend fitz Thomas, who became leader of the Munster rebels, had forewarned him. This may not necessarily have been the case: perhaps he observed his neighbour behaving suspiciously and drew his own conclusions. Moreover, successful rebellions in the rest of the country at this time made a similar outbreak in Munster all but inevitable. It is true that fitz Thomas ordered that neither Pyne nor his tenants be harmed, but this probably reflected the rebel leader's desire to retain a sympathetic contact on the English side in the event of negotiations with the crown.
Despite fitz Thomas's commands, Pyne's property and tenants were attacked by local rebels (including his erstwhile ally Patrick Condon) who inflicted losses totalling £1,800 on them. Nonetheless, Mogeely castle held out and, due to its strategic importance, soon hosted fifty royal soldiers. Meanwhile in England Pyne contracted with the crown to supply the royal forces at Youghal before returning to his castle in October 1599. Despite this being a truce period, the rebels blockaded Mogeely and plotted his assassination. For his part, Pyne sheltered Irish loyalists and English forces, significantly strengthened his fortifications, influenced local Irish lords such as David Barry to support the crown, and used his personal contacts amongst the Irish to gain intelligence on the rebels’ plans. Indeed, his popularity with the local Irish was such that the rebels were forced to forbid the provisioning of Mogeely on pain of death.
In April 1600 the government discharged its garrison at Mogeely, forcing Pyne to maintain a force there out of his own pocket, which encouraged the rebels to renew their attempts to take the castle. Then rumours emerged throwing doubts on his loyalty to the crown. Fortunately, the newly appointed president of Munster, Sir George Carew (qv), prized him as the best source of information on the disposition of the loyalist Irish, a group that no English commander could take for granted. Thus in September he went to London carrying a glowing recommendation from Carew, which enabled him to quash the suspicions surrounding his conduct and to be granted £170 in November for his services on behalf of the crown. However, the chief royal minister in London, Sir Robert Cecil, regarded him warily due to his predilection for scheming, and probably suspected him of being motivated primarily by personal financial gain; as a result, his request for a command in the royal army was unsuccessful.
Thanks to Carew's success in quelling the rebellion in Munster, Pyne was able to restart his timber business on his return to Ireland early in 1601, but he continued to attract controversy. In February Irish exchequer officials wanted him held to account for rents he had collected on behalf of the crown, and then in July Ralegh and his other partners accused him of breaking their agreement and of seizing the partnership's profits and capital worth £4,000 for his own use. The English privy council ordered a halt on any further exports of timber and summoned him to London; he angrily denied the charges, claiming that Ralegh owed him money. The losses occasioned by the fighting in Munster (1598–1600) had left all parties to the venture in financial straits: Pyne in particular had spent heavily on the defence of Mogeely and probably had siphoned off money from the partnership to do so. The matter appears to have been settled privately and no further action was taken. In March 1602 the captured Munster rebel leader and Pyne's former associate, James fitz Thomas, revealed under interrogation in London evidence suggesting Pyne had engaged in treason. He was sent a prisoner to London in April 1602 but after questioning him the authorities cleared him of any treason in December and freed him.
On his release he found that Ralegh had sold all his interests in Ireland to Richard Boyle (qv), who now became his new business partner and landlord. He found life under a resident landlord, and a particularly acquisitive and unscrupulous one at that, far less congenial. His debts put him at a disadvantage from the start, as they forced him to borrow heavily from Boyle, who tried to use this as a lever to subvert Pyne's lease of Mogeely, which Boyle held to be too long and at too cheap a rent. In particular Boyle hotly contested Pyne's claim that Ralegh had granted him an eighty-eight-year lease on Mogeely in succession to his original forty-year lease. Neither would give way and for nearly two decades they continued an acrimonious relationship. Rather surprisingly the Boyle and Pyne families appear to have been quite close, despite the animosity between their respective heads: Pyne's son Henry was employed in Boyle's iron ore factory.
Pyne suffered a bad stroke of luck in 1617 when his former landlord Ralegh, while en route to Guinea, was forced to dock and remain for some weeks at Cork due to adverse winds. During this hiatus Boyle, by loaning him money, induced Ralegh to deny that he had extended Pyne's lease. Pyne remained defiant and was vindicated in 1618 when Ralegh retracted this statement the night before his own execution. Despite holding his position at Mogeely, his hopes of expanding his commercial and landed interests in Munster were frustrated by Boyle, who prospered to become the wealthiest landowner in Ireland. Aside from his constant skirmishing with Boyle, Pyne was also engaged in a long-running legal battle with Sir Richard Fleetwood, who sought to acquire the Condon estate and with it the lease held by Pyne to parts of the Condon estate.
By 1598 Pyne appears to have married into the Stronge family of Dunkitt, Co. Kilkenny, and had at least four sons: Nicholas (his heir), Matthew, Charles, and John. He died at some point between July 1620 and October 1627.