In view of the immense calls on his time, William Henry decided to set up as a full-time consulting engineer around 1898, his two eldest sons Llewellyn and Arthur joining him, and his friend Major Philip Cardew would be his senior partner.

William Henry finally retired from the Post Office on 15 February 1899, and was subsequently made the first Freeman of Caernarvon, which he was presented with on 21 September that same year. He was made a Knight Commander of the Order of the Bath (KCB) in the Queen's Birthday Honours list, an award that his son Arthur Henry also received in the 1932 Honours List.

His third son Frank was reported as working as an electrical engineer but no longer lived in the Home Counties. He was at Caernarvon with Arthur and Llewellyn when his father was inaugurated as a Freeman, having travelled from Liverpool. Percy, the youngest son, followed his maternal Grandfather's profession and became a solicitor.

Messrs Preece and Cardew leased offices in 1899 at 8 Queen Anne's Gate, overlooking St James Park. William Henry became a member of the Board at the London Electricity Supply Company, and chairman of the British Coalite Company. He also served as President of the Institution of Civil Engineers 1898-9.

In 1901, he was elected Chair of the Society of Arts, having been a member for over 20 years, and was re-elected in 1902.

Some twenty years after being appointed an Honorary Consulting Engineer, his 48 years with the railway came to an abrupt end. In November 1904 he met General Manager Sir Charles Owen at Waterloo Station, who informed him his role would disappear under a series of economies. His reaction to this was not a good one, and provoked a rethink. He was told they would retain him on an Honorary basis, and he would also still; receive his free first-class travel pass!

His sister continued to live with the children at Wimbledon, although his two unmarried daughters , Mary ("Prissie") and Amy, preferred Penrhos, they were joined there by their now-widowed sister Agnes (wife of David Moseley) within a few years.

By 1909 William Henry was devoting less time to Preece & Cardew, and the business took on a new partner. His sons Llewellyn and Arthur continued to work for the firm, Llewellyn specialising in wireless, and Arthur with electricity undertakings, covering as far afield as the Empire, China and South America.

The winter of 1912/13 was spent in Egypt, with a trip to Bombay for good measure, despite his declining health. In mid-July he sent a donation to the Times for purchasing for the public the Sydenham Parkland on which the Crystal Palace had been re-erected, his covering letter mentioning being present at the original building's opening ceremony on 1 May 1851. However, his health continued to worsen, and by August he was back at Penrhos and confined to his room. Sadly this meant he was unable to move to sunnier climes as in the past, and he passed away on 6 November 1913.
 
The national, provincial and technical press published almost 200 obituaries. A correspondent summed up their general tenor – “the world has lost a good friend’. He wrote of walking into Preece’s room one day and telling him that machinery could be made to think, and I remember his genial and at the same time caustic reply, as he offered me a cigar and told me to ‘sit down and tell me about it’. He concluded: - ‘Society owes a great deal to Preece, more perhaps than it may ever realise’.