Doctor in Clover is another 'Doctor' movie, but this time Leslie Phillips is the main doctor in the story, looking for love and romance from the hospital nurses, much to the annoyance of the main Administrator (James Robertson Justice) who wants his doctors to be 100% focussed on the job. Numerous antics follow, with Phillips getting Justice fixed up with the new prim-and-proper Matron (Joan Sims) and his attempted failures to lure the hospital's beauty, the physiotherapist.

Dr. Gaston Grimsdyke, an accident-prone, 35-year-old philanderer who has lost his job as a prison medical officer, enrolls in the Hampden Cross Hospital medical school for a refresher course with his former professor, Sir Lancelot Spratt. There Gaston falls in love with Jeannine, a French physiotherapist, and attempts to find a job at the hospital to stay and enjoy her company. Gaston's situation is complicated by the presence of Dr. Miles Grimsdyke, his cousin, who wants the same job in order to be with Nurse Holiday. Gaston flirts with Jeannine, but she prefers the company of Lambert Symington, a handsome medical student. Instructed by the professor to "soften up" Matron Sweet, a tough middle-aged careerwoman, Gaston sends love notes to her and signs them "L. S." Matron Sweet mistakenly interprets the signature as that of old Sir Lancelot Spratt. One evening Sir Lancelot accidentally receives a rejuvenation injection meant for Gaston and causes chaos at a party when he tries to sexually assault the matron. The next morning, Matron Sweet announces her departure in order to avoid a romance that could hamper her career. Gaston dresses in mod clothing to impress Jeannine, but she still refuses to abandon Lambert for him. Sir Lancelot announces that the hospital job will be given to Miles, and as consolation to the downcast Gaston, Sir Lancelot proposes that he romance the new matron. Gaston sees the pretty young woman and cheerfully accepts the assignment.