In this paper, we present a new microstrip to waveguide transition design for interfacing printed circuit board (PCB) microstrip transmission lines with 3-D printed metallised-plastic waveguide components. Compared with traditional metal waveguides, interfacing with plastic-based waveguides are challenging due to thermal and mechanical constraints. Despite the development of 3-D printing technology, the precision of 3-D printed waveguides is not as good as the machined metal counterparts. This is critical for microwave components and must be considered in the design process. To minimise the effect of non-ideal waveguide components, a design methodology minimising sensitivity to geometrical variations in the 3-D printed parts is proposed. By sandwiching the PCB between two waveguide sections and optimising the waveguide impedance transformation geometry, the design shows very low insertion loss. It is mechanically robust, cost effective and simple to manufacture. In full system integration, this transition design eliminates the need for expensive microwave cabling and connectors by directly mounting the waveguide to the microwave transceiver PCB. The proof-of-concept transition structure presented in this paper is suitable for microwave applications where low cost and low weight are critical, for example, drone-based radars for remote sensing and space-born satellites. The fabricated structure is characterised using two sets of waveguide components manufactured with different 3-D printing technology and metallisation process': conductive spray painted Fused Deposition Modelling—Polylactic Acid (PLA Painted) and copper electroplated Stereolithography (SLA Plated). Scattering parameters for both types are measured in a short and back-to-back configuration, obtaining the reflection coefficient and insertion loss. Measurements indicate good agreement with modelling and measured performance exceeding prior art. The measured operation band of the Copper-SLA version is 2.9–7.2 GHz with <−10 dB reflection coefficient (S11) and with an insertion loss (S21) of <0.7 dB. With the reduced metallisation and surface quality of the Spray-PLA model, the band is shifted to 3.0–8.0 GHz with an increased S21 of <1.8 dB. The results demonstrate the importance of adopting new transition structures for 3-D printed microwave components where the surface roughness, metallisation quality, and mechanical properties are less optimal. By combining the proposed design with 3-D printed metallised microwave components, very light weight and cost-effective antenna systems can be implemented. Radiation measurements of a 3-D printed double ridge horn antenna connected to the waveguide and used as a feed are also presented, where the operation band is measured to 3–10 GHz with a gain of 5–10 dBi.