Ixodes ricinus is the predominant tick species in Europe and the primary pathogen vector for both humans and animals. These ticks are frequently involved in the transmission of Borrelia burgdorferi sensu lato, the causative agents of Lyme borreliosis. While much more is known about Ixodes ricinus tick-borne pathogen (TBP) composition, information about temporal TBP patterns remain scarce. These data are crucial for predicting seasonal/annual patterns which could improve understanding and prevent tick-borne diseases (TBD). We examined TBP dynamics in Ixodes ricinus collected monthly in a peri-urban forest over three consecutive years. In total, 998 nymphs were screened for 31 pathogenic species using high-throughput microfluidic real-time PCR. We detected Anaplasma phagocytophilum (5.3%), Rickettsia helvetica (4.5%), Borrelia burgdorferi s.l. (3.7%), Borrelia miyamotoi (1.2%), Babesia venatorum (1.5%), Babesia divergens (0.1%), and the agent of the cat-flea typhus, Rickettsia felis (0.1%). Among all analysed ticks, 15.9% were infected by at least one of these microorganisms, and 1.3% were co-infected. Co-infections with B. afzeli/B. garinii and B. afzelii/B. spielmanii were significantly over-represented. Moreover, significant variations in seasonal and/or inter-annual prevalence were observed for several pathogens (R. helvetica, B. burgdorferi s.l., B. miyamotoi, and A. phagocytophilum), emphasising that regularly monitoring ticks and TBP is essential to appropriately assess acarological risk.