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diff --git a/science/py-pymatgen/Makefile b/science/py-pymatgen/Makefile
index eb813481361f..d2c20a7a5deb 100644
--- a/science/py-pymatgen/Makefile
+++ b/science/py-pymatgen/Makefile
@@ -1,7 +1,6 @@
PORTNAME= pymatgen
DISTVERSIONPREFIX= v
-DISTVERSION= 2026.3.23
-PORTREVISION= 1
+DISTVERSION= 2026.5.4
CATEGORIES= science python
#MASTER_SITES= PYPI # no tests
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
@@ -15,7 +14,7 @@ LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= ${PY_SETUPTOOLS} \
- ${PYTHON_PKGNAMEPREFIX}numpy>0:math/py-numpy@${PY_FLAVOR} \
+ ${PYTHON_PKGNAMEPREFIX}numpy1>0:math/py-numpy1@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR}
RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pymatgen-core>=2026.3.9:science/py-pymatgen-core@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}certifi>=2024.8.30:security/py-certifi@${PY_FLAVOR} \
diff --git a/science/py-pymatgen/distinfo b/science/py-pymatgen/distinfo
index 4f86f328f12c..96e958390982 100644
--- a/science/py-pymatgen/distinfo
+++ b/science/py-pymatgen/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1776620172
-SHA256 (materialsproject-pymatgen-v2026.3.23_GH0.tar.gz) = 83c8bc5f92530eeec6c068a56b9530948e9944df5ed54c77625c6ba8142a22d1
-SIZE (materialsproject-pymatgen-v2026.3.23_GH0.tar.gz) = 169183015
+TIMESTAMP = 1778014183
+SHA256 (materialsproject-pymatgen-v2026.5.4_GH0.tar.gz) = 38b88397a9ccd84e40c02e8a5c5109205b93e883bc254950579facd55d50d27c
+SIZE (materialsproject-pymatgen-v2026.5.4_GH0.tar.gz) = 165423301
diff --git a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__coherent__interface.py b/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__coherent__interface.py
deleted file mode 100644
index e03965fff1f4..000000000000
--- a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__coherent__interface.py
+++ /dev/null
@@ -1,13 +0,0 @@
---- tests/analysis/interfaces/test_coherent_interface.py.orig 2026-04-20 05:45:36 UTC
-+++ tests/analysis/interfaces/test_coherent_interface.py
-@@ -46,7 +46,9 @@ class TestInterfaceBuilder(MatSciTest):
- assert len(builder.terminations) == 2
- # SP: this test is super fragile and the result fluctuates between 6, 30 and 42 for
- # no apparent reason. The author should fix this.
-- assert len(list(builder.get_interfaces(termination=("O2_Pmmm_1", "Si_R-3m_1")))) >= 6
-+ # Use the O2 termination dynamically since spglib versions can yield different suffix numbers
-+ o2_termination = next(t for t in builder.terminations if t[0].startswith("O2_"))
-+ assert len(list(builder.get_interfaces(termination=o2_termination))) >= 6
-
-
- class TestCoherentInterfaceBuilder:
diff --git a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__substrate__analyzer.py b/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__substrate__analyzer.py
deleted file mode 100644
index bb938698160c..000000000000
--- a/science/py-pymatgen/files/patch-tests_analysis_interfaces_test__substrate__analyzer.py
+++ /dev/null
@@ -1,17 +0,0 @@
---- tests/analysis/interfaces/test_substrate_analyzer.py.orig 2026-04-20 05:45:36 UTC
-+++ tests/analysis/interfaces/test_substrate_analyzer.py
-@@ -50,11 +50,11 @@ def test_generate_surface_vectors():
- assert [substrate_millers] == substrate_miller_indices
- assert_allclose(
- film_vectors,
-- [[0, 0, 3.035429], [-2.764654e-16, 4.515023, 2.764654e-16]],
-+ [[4.881342e-16, 3.035429e+00, 1.858664e-16], [4.515023e+00, 0.0, 2.764654e-16]],
- atol=1e-6,
- )
- assert_allclose(
- substrate_vectors,
-- [[-3.766937, -1.928326, -6.328967], [3.766937, -12.307154, 0.0]],
-- atol=1e-6,
-+ [[1.928326e+00, 6.328967e+00, -3.766937e+00], [1.2307154e+01, 0.0, 3.766937e+00]],
-+ atol=1e-5,
- )
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