Purpose: This study evaluated the microleakage resistance of milled and 3D-printed (3DP) polymethylmethacrylate (PMMA) provisional crowns cemented with either eugenol-based or noneugenol-based cements. Materials and methods: Forty-eight extracted human molars were prepared for full coverage crowns, scanned, and standard tessellation language (STL) files were generated for crown fabrication. Milled and 3DP PMMA crowns were divided into four groups based on the cement type: group ME (milled with eugenol-based cement), group MN (milled with noneugenol cement), group PE (3DP with eugenol-based cement), and group PN (3DP with noneugenol cement). All samples underwent thermocycling, followed by immersion in methylene blue dye to evaluate microleakage. Microleakage scores were statistically analyzed using Kruskal–Wallis and Mann–Whitney U tests with Bonferroni correction. Results: Significant differences were found across groups (p < 0.001), confirming that both crown fabrication method and cement type significantly influence microleakage resistance. Group PN showed the lowest microleakage (median score: 1, mean rank: 14.88), followed by MN (median score: 1, mean rank: 19.75), ME (median score: 2, mean rank: 30.42), and PE (median score: 2, mean rank: 32.96). Post hoc analysis indicated significantly lower microleakage for noneugenol cements compared to eugenol-based cements, especially in 3DP crowns. Conclusion: Noneugenol cements, particularly with 3DP crowns, demonstrated superior microleakage resistance, suggesting their suitability for longer-term provisional applications. Milled crowns generally showed better marginal adaptation than 3DP crowns, emphasizing the impact of both crown fabrication method and cement type on marginal seal integrity.