The four-time Olympic champion won the team sprint alongside Jason Kenny and veteran Jason Queally in a team that could compete together next year in the capital.
Kenny and Hoy are nailed on to make up two of the three slots in the team sprint at London 2012 and the 41-year-old Queally, who won gold in Sydney eleven years ago, did not do his chances of selection any harm in Manchester.
The trio fought off the challenge of Dave Daniell, who took his third silver of the week, Ross Edgar and Pete Mitchell in the final as Hoy added team sprint gold to his individual sprint and keirin titles from earlier in the week.
And the 35-year-old was in a bullish mood afterwards, demanding more from himself and his team-mates at the European Championships in Holland later this month.
“My performances have been better than I expected bearing in mind that none of us are really fresh,” he said.
“We have a couple of weeks to the Europeans where we will be looking to progress and again you would expect the performances to improve so it’s a really good starting point.
“In terms of the overall plan this is right up there with as good as I could have expected.”
Meanwhile, Becky James continued her fine form and appears a genuine threat to the absent Victoria Pendleton as she took gold in the keirin to go with her sprint title from Friday.
“Friday was awesome, I was so happy with the flying sprint,” she said.
“Today I had my head screwed on, I kept my gap and no one wanted to come round so I kept watching and then with a lap and a half to go I just hit it hard and controlled the pace.”
Elsewhere, newly-crowned Junior Road Race Champion Lucy Garner was on the podium again as she joined Harriet Owen to win gold in the Junior Women’s Madison while Jonathan Mould became the new National Omnium champion.
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