After just one season in charge of Braintree Town, Cowley moved on again, this time to Lincoln City on 13 May 2016.
During Cowley's first season in charge of Lincoln, he oversaw the club's promotion back to the Football League - doing so by winning the National League title with two games to spare. This, after a six-year absence since relegation in 2011.
In the same season Lincoln became the first non-league club to reach the quarter-final of the FA Cup in over a century, knocking out Championship sides Ipswich Town and Brighton & Hove Albion, followed by Premier League side Burnley, in the process. Lincoln eventually lost 5–0 to Arsenal in the quarter-finals. In April 2018, with their contracts due to end in 2021, Cowley and his brother signed contract extensions lasting until 2022.
On 8 April 2018, he led his team to the EFL Trophy final against Shrewsbury Town at Wembley Stadium which they won 1-0 owing to a goal by Elliott Whitehouse. It was Lincoln's first ever game at Wembley.
In Lincoln's first season back in the league (2017–18) they finished the season seventh in League Two. The following season, Cowley guided Lincoln to promotion to League One, returning to the third tier of English football for the first time since 1999. On 22 April 2019, Cowley led Lincoln as champions to League One after a 0-0 home draw to Tranmere Rovers.
Impressive record. Young, hungry English Manager. Take a punt DC.