Conjunctival swabs (CS) are the most promising non-invasive samples for the diagnosis and the regular screening of Leishmania infantum infection in dogs although knowledge on their diagnostic performance is still inconclusive. This study evaluates CS real time-PCR (qPCR) analysis for the diagnosis of canine leishmaniosis (CanL) and its prognostic value in seropositive dogs from an endemic area. In October 2020 (T0), 26 dogs were enrolled, divided in two groups according to anti-L. infantum antibody titres (n = 13, group low titre (LT) and n = 13, group high titre (HT)), and followed-up in August 2021. At both timepoints, animals underwent clinical examination, complete blood count and biochemical analyses, and serological (indirect fluorescent antibody test) and molecular (CS and peripheral blood qPCR) testing. At T0, 10 out of 26 enrolled dogs were positive at CS qPCR, with the number of positive animals significantly higher in group HT than in LT. After 10 months, only 5 out of 21 dogs that completed the trial still tested CS qPCR positive, and none of them developed an active CanL based on clinical score and antibody titre. None of the dogs required any leishmanicidal and/or leishmaniostatic treatments. This prospective study showed unsatisfying diagnostic and prognostic performances of CS qPCR analysis in L. infantum seropositive asymptomatic dogs from an endemic area.