This study was undertaken to evaluate the effect of a reproductive empowerment contraceptive counselling intervention (ARCHES) adapted to private clinics in Nairobi, Kenya on proximal outcomes of contraceptive use and covert use, self-efficacy, awareness and use of intimate partner violence (IPV) survivor services, and attitudes justifying reproductive coercion (RC) and IPV. We conducted a cluster-controlled trial among female family planning patients (N = 659) in six private clinics non-randomly assigned to ARCHES or control in and around Nairobi, Kenya. Patients completed interviews immediately before (baseline) and after (exit) treatment and at three- and six-month follow-up. We use inverse probability by treatment weighting (IPTW) applied to difference-in-differences marginal structural models to estimate the treatment effect using a modified intent-to-treat approach. After IPTW, women receiving ARCHES contraceptive counselling, relative to controls, were more likely to receive a contraceptive method at exit (86% vs. 75%, p < 0.001) and had a significantly greater relative increase in awareness of IPV services at from baseline to three- (beta 0.84, 95% CI 0.13, 1.55) and six-month follow-up (beta 0.92, 95% CI 0, 1.84) and a relative decrease in attitudes justifying RC from baseline to six-month follow-up (beta −0.34, 95% CI −0.65, −0.04). In the first evaluation of a clinic-based approach to address both RC and IPV in a low- or middle-income country (LMIC) context, we found evidence that ARCHES contraceptive counselling improved proximal outcomes related to contraceptive use and coping with RC and IPV. We recommend further study and refinement of this approach in Kenya and other LMICs. Plain Language Summary Reproductive coercion (RC) and intimate partner violence (IPV) are two forms of gender-based violence that are known to harm women’s reproductive health. While one intervention, ARCHES – Addressing Reproductive Coercion in Health Settings, has shown promise to improve contraceptive use and help women cope with RC and IPV in the United States, no approach has been proven effective in a low- or middle-income country (LMIC) context. In the first evaluation of a reproductive empowerment contraceptive counselling intervention in an LMIC setting, we found that ARCHES contraceptive counselling, relative to standard contraceptive counselling, improved proximal outcomes on contraceptive uptake, covert contraceptive use, awareness of local violence survives, and reduced attitudes justifying RC among women seeking contraceptive services in Nairobi, Kenya. Distal outcomes will be reported separately. Findings from this study support the promise of addressing RC and IPV within routine contraceptive counselling in Kenya on women’s proximal outcomes related to contraceptive use and coping with violence and coercion and should be used to inform the further study of this approach in Kenya and other LMICs.