Limestone calcined clay cement (LC3) is a promising solution for mitigating CO2 emissions in cement production by substantially replacing clinker with widely available supplementary cementitious materials. While calcination is the conventional method for activating clay, there is a growing interest in mechanical activation. Incorporating mechanically activated kaolin into LC3 formulation would offer a novel approach to producing this cement. This study aims to assess the impact of replacing calcined clay (CC) with mechanically activated clay (MC) in LC3 properties and relevant features. Accordingly, LC3 with MC substitutions ranging from 0 to 100 wt% were formulated. The resulting cements were characterised to evaluate their physicochemical properties, microstructure, strength, and pore distribution. LC3 incorporating MC exhibited comparable crystalline and amorphous phases to LC3 containing CC. However, the incorporation of MC accelerated hydration, leading to the earlier formation of carboaluminates and consumption of portlandite, alongside enhanced compressive strength at early curing stages. At 28 days, LC3 with 100 wt% of MC displayed similar compressive strength (42 MPa) to LC3 with 100 wt% of CC (40 MPa) with comparable pore distribution and microstructure. These findings validate MC's potential to substitute CC in LC3, offering an alternative for activating clay.