Herein, we describe the design of a portable device integrated with micromotors for real-time fluorescence sensing of (bio)markers. The system comprises a universal 3D printed platform to hold a commercial smartphone, which is equipped with an external magnification optical lens (20-400×) and tailor-made emission filters directly attached to the camera, an adjustable sample holder to accommodate a glass slide and laser excitation sources. On a first approach, we illustrate the suitability of the platform using magnetic Janus micromotors modified with fluorescent ZnS@CdxSe1-x quantum dots for real-time ON-OFF mercury detection. On a second approach, graphdiyne tubular catalytic micromotors modified with a rhodamine labelled affinity peptide are used for the OFF-ON detection of cholera toxin B. The micromotor-based smartphone for fluorescence sensing approach was compared to a high-performance optical microscope, and similar analytical features were obtained. This versatility allows for easy integration of micromotor fluorescence sensing strategies based on different propulsion mechanisms, allowing for its future use with a myriad of biomarkers and even multiplexed schemes.