Bowyer spent almost five years at Liverpool without securing a permanent place in the first team, yet returned a respectable 16 goals from 48 appearances. The inside-forward joined from Earlestown in March 1907, having previously played for Rudheath Albion, Lostock Gralam and Witton Albion. He was still only nineteen when he made his Liverpool debut in a 4–0 defeat at Manchester United on 7 September 1907. Opportunities initially came sparingly. Bowyer played four league matches and one FA Cup tie in his first season, and had to wait until 1 October 1908 for his first senior goal. Playing on the left wing at Nottingham Forest, he put Liverpool ahead, but an early injury to defender Tom Rogers left the visitors short-handed and they eventually lost 5–1. Bowyer became more involved during 1908/09, scoring four times in fourteen league appearances. His best league return followed in 1909/10, when he scored six goals in just twelve matches.
Contemporary assessments suggest a willing and energetic forward whose finishing did not always match the quality of his approach play. After Liverpool drew 2–2 at Middlesbrough on 5 November 1910, the Evening Express praised the enthusiasm Bowyer brought to the attack while acknowledging some indifferent shooting. He nevertheless scored the equaliser from Arthur Goddard’s cross, helping Liverpool become the first visiting side to take a league point at Ayrsome Park that season. Goddard supplied him again the following Saturday, when Liverpool defeated Preston North End 3–0 at Anfield. After a prolonged struggle to break down the visitors, Liverpool scored all three goals in the closing stages. For the third, Goddard advanced from halfway, evaded the keeper and passed across for Bowyer to finish. Such moments demonstrated his usefulness, even as reports continued to criticise the inside-forwards’ wastefulness.
Bowyer’s most memorable contribution came against Gainsborough Trinity in the FA Cup on 14 January 1911. A month after the club programme had criticised his accuracy, he scored twice in quick succession near the beginning of the match. Those early goals proved valuable: Gainsborough fought back, and Liverpool needed a further goal from Goddard to secure a narrow 3–2 victory. Bowyer’s double accounted for both of his FA Cup goals for the club. By 1911/12, however, he had slipped out of the first-team picture, making only two league appearances. Bristol City offered a fresh opportunity in February 1912. The Hull Daily Mail reported on 16 February that manager Sam Hollis had travelled to Liverpool to complete the transfer and that Bowyer would play at Gainsborough the following day. Appropriately, the opponents against whom he had enjoyed his finest Liverpool cup afternoon also supplied the setting for his Bristol City debut: he scored in a 3–2 away victory.
Regular football followed at Ashton Gate. Bowyer scored five goals in thirteen league appearances during the remainder of 1911/12, then nine in thirty-six matches the following season. He also returned to Anfield as Bristol City’s inside-left in the FA Cup on 15 January 1913, although Liverpool won 3–0. His Bristol career brought fourteen goals in forty-nine league appearances before he moved to South Liverpool in 1913.